From ab483cb47ba1cadf1908c47db776692d4156af78 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Mar 2014 13:47:41 +0100 Subject: [PATCH 001/722] add subversion v1.6.23 as build dep for Python 2.5.6, add easyconfigs for subversion + deps --- .../APR-util-1.5.3-goalf-1.1.0-no-OFED.eb | 23 ++++++++++++ .../APR-util-1.5.3-gompi-1.4.12-no-OFED.eb | 23 ++++++++++++ .../a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb | 23 ++++++++++++ .../a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb | 23 ++++++++++++ .../a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb | 23 ++++++++++++ .../a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb | 23 ++++++++++++ .../a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb | 23 ++++++++++++ .../a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb | 17 +++++++++ .../a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb | 17 +++++++++ .../a/APR/APR-1.5.0-goolf-1.4.10.eb | 17 +++++++++ .../a/APR/APR-1.5.0-ictce-4.0.6.eb | 17 +++++++++ .../a/APR/APR-1.5.0-ictce-4.1.13.eb | 17 +++++++++ .../a/APR/APR-1.5.0-ictce-5.2.0.eb | 17 +++++++++ .../a/APR/APR-1.5.0-ictce-5.3.0.eb | 17 +++++++++ .../libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 22 ++++++++++++ ...libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 27 ++++++++++++++ .../l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb | 22 ++++++++++++ .../n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb | 24 +++++++++++++ .../neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb | 24 +++++++++++++ .../n/neon/neon-0.30.0-goolf-1.4.10.eb | 24 +++++++++++++ .../n/neon/neon-0.30.0-ictce-4.0.6.eb | 24 +++++++++++++ .../n/neon/neon-0.30.0-ictce-4.1.13.eb | 24 +++++++++++++ .../n/neon/neon-0.30.0-ictce-5.2.0.eb | 24 +++++++++++++ .../n/neon/neon-0.30.0-ictce-5.3.0.eb | 24 +++++++++++++ .../Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 4 +++ .../Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 4 +++ .../Python/Python-2.5.6-goolf-1.4.10-bare.eb | 4 +++ .../p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 4 +++ .../Python/Python-2.5.6-ictce-4.1.13-bare.eb | 4 +++ .../p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 4 +++ .../p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 4 +++ .../SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb | 35 +++++++++++++++++++ .../SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb | 35 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb | 35 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb | 35 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb | 35 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb | 35 +++++++++++++++++++ .../subversion-1.6.23-goalf-1.1.0-no-OFED.eb | 28 +++++++++++++++ .../subversion-1.6.23-gompi-1.4.12-no-OFED.eb | 28 +++++++++++++++ .../subversion-1.6.23-goolf-1.4.10.eb | 28 +++++++++++++++ .../subversion-1.6.23-ictce-4.0.6.eb | 28 +++++++++++++++ .../subversion-1.6.23-ictce-4.1.13.eb | 28 +++++++++++++++ .../subversion-1.6.23-ictce-5.2.0.eb | 28 +++++++++++++++ .../subversion-1.6.23-ictce-5.3.0.eb | 28 +++++++++++++++ .../subversion-1.8.8-goolf-1.4.10.eb | 28 +++++++++++++++ .../subversion-1.8.8-ictce-4.1.13.eb | 28 +++++++++++++++ .../subversion-1.8.8-ictce-5.5.0.eb | 28 +++++++++++++++ .../t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb | 19 ++++++++++ .../t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb | 19 ++++++++++ .../t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb | 19 ++++++++++ .../t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb | 19 ++++++++++ .../t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb | 19 ++++++++++ 53 files changed, 1167 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb create mode 100755 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb create mode 100755 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb create mode 100755 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb create mode 100755 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..f2b2f6d4d4 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..f5f429b778 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..f2b44bb9a1 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb new file mode 100644 index 0000000000..6785705751 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb new file mode 100644 index 0000000000..ab0ac9c226 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb new file mode 100644 index 0000000000..669555d663 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb new file mode 100644 index 0000000000..5820665193 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb @@ -0,0 +1,23 @@ +name = 'APR-util' +version = '1.5.3' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('APR', '1.5.0')] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..42d75b76df --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..c9b38d32bc --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..e069e515a2 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb new file mode 100644 index 0000000000..bb13d21a33 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb new file mode 100644 index 0000000000..c26ce2075a --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb new file mode 100644 index 0000000000..3f74bca0b9 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..7c6b787d78 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'APR' +version = '1.5.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..6e4ab86218 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100755 index 0000000000..d68ae2eaee --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.5' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb new file mode 100644 index 0000000000..232c2e480f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..f111e9310e --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..212229e999 --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..dbf0e6619b --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb new file mode 100644 index 0000000000..fdf1eabe1a --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb new file mode 100644 index 0000000000..97eea6a566 --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb new file mode 100644 index 0000000000..244a91df81 --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..6dd467a1fe --- /dev/null +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb @@ -0,0 +1,24 @@ +name = 'neon' +version = '0.30.0' + +homepage = 'http://www.webdav.org/neon/' +description = "neon is an HTTP and WebDAV client library, with a C interface." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [homepage] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), +] + +configopts = "--with-libxml2" + +sanity_check_paths = { + 'files': ["bin/neon-config", "lib/libneon.a"], + 'dirs': ["include/neon"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index 279bdd8c99..6bc189fb19 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -19,6 +19,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index f9f346f7bc..ba4c8ccf22 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -19,6 +19,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index 66cb466a25..9074876929 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -19,6 +19,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index 781b45ed3f..8df72e769a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -21,6 +21,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index c8bc196270..6fde08c369 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -21,6 +21,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index 79512f826c..a35457f6ec 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -19,6 +19,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index f949db90c2..99ba7a0a56 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -19,6 +19,10 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] +# Python 2.5 requires an old subversion version to build correctly, +# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' +builddependencies = [('subversion', '1.6.23')] + osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..1f9d380786 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..330ea91aef --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..72c8d21c52 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb new file mode 100644 index 0000000000..8ab8985748 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb new file mode 100644 index 0000000000..6948614b01 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb new file mode 100644 index 0000000000..6a16570c53 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..499e33114e --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.4.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..10fcdfa9b8 --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..18b01448ee --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb new file mode 100644 index 0000000000..c4f4b6ed90 --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb new file mode 100644 index 0000000000..cc7766f42b --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb new file mode 100644 index 0000000000..0e7556d3dd --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb new file mode 100644 index 0000000000..3dd8117f6f --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb new file mode 100644 index 0000000000..8b59c05878 --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.6.23' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb new file mode 100644 index 0000000000..5f9488ba6c --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.8.8' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb new file mode 100644 index 0000000000..672480bf95 --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.8.8' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb new file mode 100644 index 0000000000..17a3d6e7d2 --- /dev/null +++ b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb @@ -0,0 +1,28 @@ +name = 'subversion' +version = '1.8.8' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://archive.apache.org/dist/subversion/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +dependencies = [ + ('APR', '1.5.0'), + ('APR-util', '1.5.3'), + ('SQLite', '3.8.4.1'), + ('zlib', '1.2.7'), + ('neon', '0.30.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..688b7db304 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..bf05390914 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb new file mode 100755 index 0000000000..4497a53f78 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb new file mode 100755 index 0000000000..a112f672e2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb new file mode 100755 index 0000000000..d9d3d41205 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From 3c41da9803d064e8e7ecdfafcc408551072ef28f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Mar 2014 17:02:30 +0100 Subject: [PATCH 002/722] drop subversion v1.8.8 ictce/5.5.0 easyconfig --- .../subversion-1.8.8-ictce-5.5.0.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb deleted file mode 100644 index 17a3d6e7d2..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-5.5.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.8.8' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '5.5.0'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' -- GitLab From 8d87638c6dd193e9b7950b4bfdf5f929f624b150 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 12:25:14 +0300 Subject: [PATCH 003/722] Adding CP2K v.2.4.0 and CP2K with i-pi --- .../c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 37 ++ .../c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb | 35 ++ .../easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch | 509 ++++++++++++++++++ .../c/CP2K/fix_compile_date_lastcvs.patch | 11 +- 4 files changed, 585 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb new file mode 100644 index 0000000000..8c26b632c2 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -0,0 +1,37 @@ +name = 'CP2K' +version = '2.4.0' +versionsuffix = '-ipi' + +homepage = 'http://www.cp2k.org' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, + to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. + It provides a general framework for different methods such as e.g. density functional theory (DFT) + using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/cp2k/files/'] + +sources = ['%s-%s.tar.bz2' % (name.lower(), version)] + +patches = [ + 'cp2k-2.4.0_ipi.patch', + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' + ] + +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5') + ] + +dependencies = [('Libint', '1.1.4')] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# about 100 tests fail +ignore_regtest_fails=True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..9389d88e83 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +name = 'CP2K' +version = '2.4.0' + +homepage = 'http://www.cp2k.org' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, + to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. + It provides a general framework for different methods such as e.g. density functional theory (DFT) + using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/cp2k/files/'] + +sources = ['%s-%s.tar.bz2' % (name.lower(), version)] + +patches = [ + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' + ] + +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5') + ] + +dependencies = [('Libint', '1.1.4')] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# about 100 tests fail +ignore_regtest_fails=True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch b/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch new file mode 100644 index 0000000000..ba7ceaf26e --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch @@ -0,0 +1,509 @@ +diff -rupN cp2k-2.4.0_ref/makefiles/Makefile cp2k-2.4.0/makefiles/Makefile +--- cp2k-2.4.0_ref/makefiles/Makefile 2013-08-15 10:46:04.535899216 +0100 ++++ cp2k-2.4.0/makefiles/Makefile 2013-08-15 10:53:45.827911028 +0100 +@@ -354,7 +354,7 @@ else + LIB_OBJECTS = + endif + +-$(LIB_CP2K_ARCHIVE): $(OBJECTS) ++$(LIB_CP2K_ARCHIVE): $(OBJECTS) sockets.o + $(AR) $(LIB_CP2K_ARCHIVE) $? + ifneq ($(RANLIB),) + $(RANLIB) $(LIB_CP2K_ARCHIVE) +diff -rupN cp2k-2.4.0_ref/src/cp2k_runs.F cp2k-2.4.0/src/cp2k_runs.F +--- cp2k-2.4.0_ref/src/cp2k_runs.F 2013-08-15 10:46:04.091899205 +0100 ++++ cp2k-2.4.0/src/cp2k_runs.F 2013-08-15 10:56:31.715915275 +0100 +@@ -73,10 +73,10 @@ MODULE cp2k_runs + USE input_constants, ONLY: & + bsse_run, cell_opt_run, debug_run, do_atom, do_band, do_cp2k, do_ep, & + do_farming, do_fist, do_mixed, do_opt_basis, do_optimize_input, & +- do_qmmm, do_qs, do_tamc, do_test, ehrenfest, electronic_spectra_run, & +- energy_force_run, energy_run, geo_opt_run, linear_response_run, & +- mol_dyn_run, mon_car_run, none_run, pint_run, real_time_propagation, & +- vib_anal ++ do_qmmm, do_qs, do_tamc, do_test, driver_run, ehrenfest, & ++ electronic_spectra_run, energy_force_run, energy_run, geo_opt_run, & ++ linear_response_run, mol_dyn_run, mon_car_run, none_run, pint_run, & ++ real_time_propagation, vib_anal + USE input_cp2k, ONLY: create_cp2k_input_reading,& + create_cp2k_root_section,& + create_global_section,& +@@ -117,6 +117,7 @@ MODULE cp2k_runs + USE timings, ONLY: timeset,& + timestop + USE vibrational_analysis, ONLY: vb_anal ++ USE driver, ONLY: run_driver + #include "cp_common_uses.h" + + IMPLICIT NONE +@@ -362,6 +363,8 @@ CONTAINS + error=suberror) + CASE (mol_dyn_run) + CALL qs_mol_dyn ( force_env, globenv, error=suberror ) ++ CASE (driver_run) ++ CALL run_driver ( force_env, globenv, error=suberror ) + CASE (geo_opt_run) + CALL cp_geo_opt(force_env,globenv,error=suberror) + CASE (cell_opt_run) +diff -rupN cp2k-2.4.0_ref/src/driver.F cp2k-2.4.0/src/driver.F +--- cp2k-2.4.0_ref/src/driver.F 1970-01-01 01:00:00.000000000 +0100 ++++ cp2k-2.4.0/src/driver.F 2013-08-15 15:43:44.895650242 +0100 +@@ -0,0 +1,216 @@ ++! ***************************************************************************** ++!> \brief Driver mode - To communicate with i-PI Python wrapper ++!> \par History ++!> none ++!> \author Michele Ceriotti 03.2012 ++! ***************************************************************************** ++MODULE driver ++ ++ USE force_env_methods, ONLY: force_env_calc_energy_force ++ USE force_env_types, ONLY: force_env_get,& ++ force_env_type, & ++ force_env_set_cell ++ USE kinds, ONLY: default_path_length,& ++ dp ++ USE input_section_types, ONLY: section_vals_get_subs_vals,& ++ section_vals_type,& ++ section_vals_val_get ++ ++ USE cell_types, ONLY: cell_clone,& ++ cell_create,& ++ cell_release,& ++ cell_type,& ++ compare_cells,& ++ init_cell,& ++ real_to_scaled,& ++ scaled_to_real ++ USE global_types, ONLY: global_environment_type ++ USE f77_interface, ONLY: default_para_env ++ USE cp_external_control, ONLY: external_control ++ USE message_passing, ONLY: mp_bcast, mp_sync ++ USE cp_subsys_types, ONLY: cp_subsys_release,& ++ cp_subsys_type ++ USE iso_c_binding ++ USE virial_types, ONLY: virial_type ++#include "cp_common_uses.h"t ++ ++ IMPLICIT NONE ++ ++ interface ++ subroutine usleep(useconds) bind(C) ++ ! integer(c_int) function usleep(useconds) bind(C) ++ use iso_c_binding ++ implicit none ++ integer(c_int32_t), value :: useconds ++ ! end function ++ end subroutine ++ end interface ++ ++ CONTAINS ++ SUBROUTINE run_driver ( force_env, globenv, error ) ++ TYPE(force_env_type), POINTER :: force_env ++ TYPE(global_environment_type), POINTER :: globenv ++ TYPE(cp_error_type), INTENT(inout) :: error ++ ++ TYPE(section_vals_type), POINTER :: drv_section, motion_section ++ TYPE(virial_type), POINTER :: virial ++ ++ CHARACTER(len=default_path_length) :: drv_hostname, c_hostname ++ INTEGER :: drv_port ++ LOGICAL :: drv_unix ++ ++ !MIK DRIVER ++ ! server address parsing ++ CHARACTER*1024 :: serveraddr, host ++ INTEGER socket, port, inet, nread, readbuffer, slock, swait, uwait ++ ! buffers and temporaries for communication ++ INTEGER, PARAMETER :: MSGLEN=12 ++ LOGICAL :: isinit=.true., hasdata=.false., ionode=.false. ++ CHARACTER*12 :: header ++ CHARACTER*1024 :: parbuffer ++ INTEGER nat ++ REAL *8 :: cellh(3,3), cellih(3,3), vir(3,3), pot ++ REAL*8, ALLOCATABLE :: combuf(:) ++ REAL*8 :: sigma(3,3) ++ ! access cp2k structures ++ TYPE(cp_subsys_type), POINTER :: subsys ++ integer ip, ii, idir ++ TYPE(cell_type), POINTER :: cpcell ++ logical should_stop ++ ionode=(default_para_env%source==default_para_env%mepos) ++ ++ ! reads driver parameters from input ++ motion_section => section_vals_get_subs_vals(force_env%root_section,"MOTION",error=error) ++ drv_section => section_vals_get_subs_vals(motion_section,"DRIVER",error=error) ++ ++ CALL section_vals_val_get(drv_section,"HOST",c_val=drv_hostname,error=error) ++ CALL section_vals_val_get(drv_section,"PORT",i_val=drv_port,error=error) ++ CALL section_vals_val_get(drv_section,"UNIX",l_val=drv_unix,error=error) ++ ++ ++ ! opens the socket ++ socket=0 ++ inet=1 ++ if (ionode) then ++ write(*,*) "@ i-PI DRIVER BEING LOADED" ++ write(*,*) "@ INPUT DATA: ", TRIM(drv_hostname), drv_port, drv_unix ++ c_hostname=TRIM(drv_hostname)//achar(0) ++ CALL open_socket(socket, .not. drv_unix, drv_port, c_hostname) ++ endif ++ ++ !now we have a socket, so we can initialize the CP2K environments. ++ NULLIFY(cpcell) ++ call cell_create(cpcell,error=error) ++ uwait=10000 ! number of MICROseconds to be waited in filesystem lock ++ driver_loop: DO ++ ! do communication on master node only... ++ header = "" ++ ++ ! this syncs the processes, possibly (see sockets.c) without calling MPI_Barrier, ++ ! which is nice as MPI_barrier eats up a lot of CPU for nothing ++ inet=slock(default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ ++ if (ionode) nread=readbuffer(socket, header, MSGLEN) ++ if (ionode) write(0,*) "returned from readbuffer" ++ ++ inet=swait(uwait, default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ ++ call mp_bcast(nread,default_para_env%source, default_para_env%group) ++ if (nread .eq. 0) then ++ if (ionode) write(*,*) " @ DRIVER MODE: Could not read from socket, exiting now." ++ exit ++ endif ++ ++ call mp_bcast(header,default_para_env%source, default_para_env%group) ++ ++ if (ionode) write(*,*) " @ DRIVER MODE: Message from server: ", trim(header) ++ if (trim(header) == "STATUS") then ++ ++ inet=slock(default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ if (ionode) then ! does not need init (well, maybe it should, just to check atom numbers and the like... ) ++ if (hasdata) then ++ call writebuffer(socket,"HAVEDATA ",MSGLEN) ++ else ++ call writebuffer(socket,"READY ",MSGLEN) ++ endif ++ endif ++ inet=swait(uwait,default_para_env%source, default_para_env%mepos) ++ CALL mp_sync(default_para_env%group) ++ else if (trim(header) == "POSDATA") then ++ if (ionode) then ++ nread=readbuffer(socket, cellh, 9*8) ++ nread=readbuffer(socket, cellih, 9*8) ++ nread=readbuffer(socket, nat, 4) ++ cellh=transpose(cellh) ++ cellih=transpose(cellih) ++ endif ++ call mp_bcast(cellh,default_para_env%source, default_para_env%group) ++ call mp_bcast(cellih,default_para_env%source, default_para_env%group) ++ call mp_bcast(nat,default_para_env%source, default_para_env%group) ++ if (.not.allocated(combuf)) allocate(combuf(3*nat)) ++ if (ionode) nread=readbuffer(socket, combuf, nat*3*8) ++ call mp_bcast(combuf,default_para_env%source, default_para_env%group) ++ ++ CALL force_env_get(force_env,subsys=subsys,error=error) ++ if (nat/=subsys%particles%n_els) WRITE(*,*) " @DRIVER MODE: Uh-oh! Particle number mismatch between i-pi and cp2k input!" ++ ii=0 ++ DO ip=1,subsys%particles%n_els ++ DO idir=1,3 ++ ii=ii+1 ++ subsys%particles%els(ip)%r(idir)=combuf(ii) ++ END DO ++ END DO ++ CALL init_cell(cpcell, hmat=cellh) ++ CALL force_env_set_cell(force_env,cell=cpcell,error=error) ++ ++ CALL force_env_calc_energy_force(force_env,calc_force=.TRUE. ,error=error) ++ ++ if (ionode) write(*,*) " @ DRIVER MODE: Received positions " ++ ++ combuf=0 ++ ii=0 ++ DO ip=1,subsys%particles%n_els ++ DO idir=1,3 ++ ii=ii+1 ++ combuf(ii)=subsys%particles%els(ip)%f(idir) ++ END DO ++ END DO ++ CALL force_env_get(force_env, potential_energy=pot, error=error) ++ CALL force_env_get(force_env,cell=cpcell, virial=virial, error=error) ++ vir = transpose(virial%pv_virial) ++ ++ CALL external_control(should_stop,"DPI",globenv=globenv,error=error) ++ IF (should_stop) EXIT ++ ++ hasdata=.true. ++ else if (trim(header)=="GETFORCE") then ++ if (ionode) write(*,*) " @ DRIVER MODE: Returning v,forces,stress " ++ if (ionode) then ++ call writebuffer(socket,"FORCEREADY ",MSGLEN) ++ call writebuffer(socket,pot,8) ++ call writebuffer(socket,nat,4) ++ call writebuffer(socket,combuf,3*nat*8) ++ call writebuffer(socket,vir,9*8) ++ ++ ! i-pi can also receive an arbitrary string, that will be printed out to the "extra" ++ ! trajectory file. this is useful if you want to return additional information, e.g. ++ ! atomic charges, wannier centres, etc. one must return the number of characters, then ++ ! the string. here we just send back zero characters. ++ nat=0 ++ call writebuffer(socket,nat,4) ! writes out zero for the length of the "extra" field (not implemented yet!) ++ endif ++ hasdata=.false. ++ else ++ if (ionode) write(*,*) " @DRIVER MODE: Socket disconnected, time to exit. " ++ exit ++ endif ++ ENDDO driver_loop ++ ++ END SUBROUTINE run_driver ++ ++END MODULE driver ++ ++ +diff -rupN cp2k-2.4.0_ref/src/input_constants.F cp2k-2.4.0/src/input_constants.F +--- cp2k-2.4.0_ref/src/input_constants.F 2013-08-15 10:46:04.107899205 +0100 ++++ cp2k-2.4.0/src/input_constants.F 2013-08-15 10:53:45.839911028 +0100 +@@ -135,7 +135,8 @@ MODULE input_constants + cell_opt_run=14,& + real_time_propagation=15,& + ehrenfest=16, & +- do_tamc=17 ++ do_tamc=17, & ++ driver_run=18 + + ! Run Types of Atom Code + INTEGER, PARAMETER, PUBLIC :: atom_no_run=1,& +diff -rupN cp2k-2.4.0_ref/src/input_cp2k.F cp2k-2.4.0/src/input_cp2k.F +--- cp2k-2.4.0_ref/src/input_cp2k.F 2013-08-15 10:46:04.131899206 +0100 ++++ cp2k-2.4.0/src/input_cp2k.F 2013-08-15 10:53:45.843911028 +0100 +@@ -422,13 +422,13 @@ CONTAINS + "BAND", "CELL_OPT", "WFN_OPT", "WAVEFUNCTION_OPTIMIZATION",& + "MOLECULAR_DYNAMICS", "GEOMETRY_OPTIMIZATION", "MONTECARLO",& + "ELECTRONIC_SPECTRA", "LINEAR_RESPONSE", "NORMAL_MODES","RT_PROPAGATION",& +- "EHRENFEST_DYN","TAMC" ),& ++ "EHRENFEST_DYN","TAMC","DRIVER" ),& + enum_i_vals=(/ none_run, energy_run, energy_force_run, mol_dyn_run,& + geo_opt_run, mon_car_run, electronic_spectra_run, debug_run,& + bsse_run, linear_response_run, pint_run, vib_anal,do_band,& + cell_opt_run, energy_run, energy_run, mol_dyn_run, geo_opt_run,& + mon_car_run, electronic_spectra_run, linear_response_run,& +- vib_anal,real_time_propagation,ehrenfest,do_tamc/),& ++ vib_anal,real_time_propagation,ehrenfest,do_tamc,driver_run/),& + enum_desc=s2a("Perform no tasks", "Computes energy","Computes energy and forces",& + "Molecular Dynamics","Geometry Optimization","Monte Carlo", "Computes absorption Spectra",& + "Performs a Debug analysis","Basis set superposition error","Linear Response",& +@@ -437,7 +437,7 @@ CONTAINS + "Alias for MC","Alias for SPECTRA","Alias for LR","Alias for VIBRATIONAL_ANALYSIS",& + "Real Time propagation run (fixed ionic positions)",& + "Ehrenfest dynamics (using real time propagation of the wavefunction)",& +- "TAMC"),& ++ "TAMC","i-PI driver mode"),& + supported_feature=.TRUE.,error=error) + CALL section_add_keyword(section,keyword,error=error) + CALL keyword_release(keyword,error=error) +diff -rupN cp2k-2.4.0_ref/src/input_cp2k_motion.F cp2k-2.4.0/src/input_cp2k_motion.F +--- cp2k-2.4.0_ref/src/input_cp2k_motion.F 2013-08-15 10:46:04.095899205 +0100 ++++ cp2k-2.4.0/src/input_cp2k_motion.F 2013-08-15 10:53:45.843911028 +0100 +@@ -103,6 +103,10 @@ CONTAINS + CALL section_add_subsection(section,subsection,error=error) + CALL section_release(subsection,error=error) + ++ CALL create_driver_section(subsection,error=error) ++ CALL section_add_subsection(section,subsection,error=error) ++ CALL section_release(subsection,error=error) ++ + CALL create_fe_section(subsection,error=error) + CALL section_add_subsection(section, subsection, error=error) + CALL section_release(subsection,error=error) +@@ -1713,6 +1717,59 @@ CONTAINS + END SUBROUTINE create_md_section + + ! ***************************************************************************** ++!> \param section will contain the driver section ++!> \param error variable to control error logging, stopping,... ++!> see module cp_error_handling ++!> \author mceriotti ++! ***************************************************************************** ++ SUBROUTINE create_driver_section(section,error) ++ TYPE(section_type), POINTER :: section ++ TYPE(cp_error_type), INTENT(inout) :: error ++ ++ CHARACTER(len=*), PARAMETER :: routineN = 'create_driver_section', & ++ routineP = moduleN//':'//routineN ++ ++ LOGICAL :: failure ++ TYPE(keyword_type), POINTER :: keyword ++ ++ failure=.FALSE. ++ ++ CPPrecondition(.NOT.ASSOCIATED(section),cp_failure_level,routineP,error,failure) ++ IF (.NOT. failure) THEN ++ CALL section_create(section,name="DRIVER",& ++ description="This section defines the parameters needed to run in i-PI driver mode.",& ++ n_keywords=3, n_subsections=0, repeats=.FALSE., required=.TRUE.,& ++ error=error) ++ ++ NULLIFY(keyword) ++ CALL keyword_create(keyword, name="unix",& ++ description="Use a UNIX socket rather than an INET socket.",& ++ usage="unix LOGICAL",& ++ default_l_val=.FALSE., lone_keyword_l_val=.TRUE., error=error) ++ CALL section_add_keyword(section,keyword,error=error) ++ CALL keyword_release(keyword,error=error) ++ ++ CALL keyword_create(keyword, name="port",& ++ description="Port number for the i-PI server.",& ++ usage="port ",& ++ default_i_val=12345, error=error) ++ CALL section_add_keyword(section,keyword,error=error) ++ CALL keyword_release(keyword,error=error) ++ ++ ++ CALL keyword_create(keyword, name="host",& ++ description="Host name for the i-PI server.",& ++ usage="host ",& ++ default_c_val="localhost", error=error) ++ CALL section_add_keyword(section,keyword,error=error) ++ CALL keyword_release(keyword,error=error) ++ ++ END IF ++ ++ END SUBROUTINE create_driver_section ++ ++ ++! ***************************************************************************** + !> \brief Defines AVERAGES section + !> \param error variable to control error logging, stopping,... + !> see module cp_error_handling +diff -rupN cp2k-2.4.0_ref/src/OBJECTDEFS cp2k-2.4.0/src/OBJECTDEFS +--- cp2k-2.4.0_ref/src/OBJECTDEFS 2013-08-15 10:46:04.091899205 +0100 ++++ cp2k-2.4.0/src/OBJECTDEFS 2013-08-15 10:53:45.843911028 +0100 +@@ -180,6 +180,7 @@ OBJECTS_GENERIC =\ + dm_ls_scf.o\ + dm_ls_scf_qs.o\ + dm_ls_scf_types.o\ ++ driver.o\ + efield_utils.o\ + eigenvalueproblems.o\ + eip_environment.o\ +diff -rupN cp2k-2.4.0_ref/src/sockets.c cp2k-2.4.0/src/sockets.c +--- cp2k-2.4.0_ref/src/sockets.c 1970-01-01 01:00:00.000000000 +0100 ++++ cp2k-2.4.0/src/sockets.c 2013-08-15 15:27:36.971625458 +0100 +@@ -0,0 +1,112 @@ ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++ ++ ++//#define FS_WAIT 1 // uncomment to use a file system lock rather than mpi_barrier. ++ ++void error(const char *msg) ++{ perror(msg); } ++ ++void open_socket_(int *psockfd, int* inet, int* port, char* host) // the darn fortran passes an extra argument for the string length. here I just ignore it ++{ ++ int sockfd, portno, n; ++ struct hostent *server; ++ ++ fprintf(stderr, "Connection requested %s, %d, %d\n", host, *port, *inet); ++ struct sockaddr * psock; int ssock; ++ if (*inet!=0) ++ { ++ struct sockaddr_in serv_addr; psock=(struct sockaddr *)&serv_addr; ssock=sizeof(serv_addr); ++ sockfd = socket(AF_INET, SOCK_STREAM, 0); ++ if (sockfd < 0) error("ERROR opening socket"); ++ ++ server = gethostbyname(host); ++ if (server == NULL) ++ { ++ fprintf(stderr, "ERROR, no such host %s \n", host); ++ exit(-1); ++ } ++ ++ bzero((char *) &serv_addr, sizeof(serv_addr)); ++ serv_addr.sin_family = AF_INET; ++ bcopy((char *)server->h_addr, (char *)&serv_addr.sin_addr.s_addr, server->h_length); ++ serv_addr.sin_port = htons(*port); ++ } ++ else ++ { ++ struct sockaddr_un serv_addr; psock=(struct sockaddr *)&serv_addr; ssock=sizeof(serv_addr); ++ sockfd = socket(AF_UNIX, SOCK_STREAM, 0); ++ bzero((char *) &serv_addr, sizeof(serv_addr)); ++ serv_addr.sun_family = AF_UNIX; ++ strcpy(serv_addr.sun_path, "/tmp/ipi_"); ++ strcpy(serv_addr.sun_path+9, host); ++ } ++ ++ if (connect(sockfd, psock, ssock) < 0) error("ERROR connecting"); ++ ++ *psockfd=sockfd; ++} ++ ++void writebuffer_(int *psockfd, char *data, int* plen) ++{ ++ int n; ++ int sockfd=*psockfd; ++ int len=*plen; ++ ++ n = write(sockfd,data,len); ++ if (n < 0) error("ERROR writing to socket\n"); ++} ++ ++ ++int readbuffer_(int *psockfd, char *data, int* plen) ++{ ++ int n, nr; ++ int sockfd=*psockfd; ++ int len=*plen; ++ ++ n = nr = read(sockfd,data,len); ++ ++ while (nr>0 && n Date: Thu, 7 Aug 2014 14:37:19 +0300 Subject: [PATCH 004/722] Adding modified configs and patch file --- .../c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 20 +++++++++---------- .../c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb | 18 ++++++++--------- .../easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch | 1 + 3 files changed, 20 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index 8c26b632c2..567f926654 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -4,9 +4,9 @@ versionsuffix = '-ipi' homepage = 'http://www.cp2k.org' description = """CP2K is a freely available (GPL) program, written in Fortran 95, - to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. - It provides a general framework for different methods such as e.g. density functional theory (DFT) - using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ + to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. + It provides a general framework for different methods such as e.g. density functional theory (DFT) + using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -15,15 +15,15 @@ source_urls = ['http://sourceforge.net/projects/cp2k/files/'] sources = ['%s-%s.tar.bz2' % (name.lower(), version)] patches = [ - 'cp2k-2.4.0_ipi.patch', - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch' - ] + 'cp2k-2.4.0_ipi.patch', + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' + ] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') + ] dependencies = [('Libint', '1.1.4')] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb index 9389d88e83..d44d72b4be 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb @@ -3,9 +3,9 @@ version = '2.4.0' homepage = 'http://www.cp2k.org' description = """CP2K is a freely available (GPL) program, written in Fortran 95, - to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. - It provides a general framework for different methods such as e.g. density functional theory (DFT) - using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ + to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. + It provides a general framework for different methods such as e.g. density functional theory (DFT) + using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -14,14 +14,14 @@ source_urls = ['http://sourceforge.net/projects/cp2k/files/'] sources = ['%s-%s.tar.bz2' % (name.lower(), version)] patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch' - ] + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' + ] builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] + ('flex', '2.5.35'), + ('Bison', '2.5') + ] dependencies = [('Libint', '1.1.4')] diff --git a/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch b/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch index ba7ceaf26e..b8115df6c5 100644 --- a/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch +++ b/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch @@ -1,3 +1,4 @@ +#This patch makes CP2K source code compatible with i-pi diff -rupN cp2k-2.4.0_ref/makefiles/Makefile cp2k-2.4.0/makefiles/Makefile --- cp2k-2.4.0_ref/makefiles/Makefile 2013-08-15 10:46:04.535899216 +0100 +++ cp2k-2.4.0/makefiles/Makefile 2013-08-15 10:53:45.827911028 +0100 -- GitLab From 8b85e2f64d3e0a3ceed8e38ce49f973f50b7219e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Dec 2014 19:34:11 +0100 Subject: [PATCH 005/722] add easyconfig for ROOT v5.30.06 with goolf toolchain --- ...libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 27 ++++++++++++++ .../r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb | 35 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb create mode 100755 easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..d68ae2eaee --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.5' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb new file mode 100755 index 0000000000..9a78780f34 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +name = 'ROOT' +version = 'v5.30.06' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] + +python = 'Python' +pyver = '2.7.5' + +dependencies = [ + ('GSL', '1.16'), + ('libxml2', '2.9.1', '-%s-%s' % (python, pyver)), + (python, pyver), +] + +# architecture +arch = 'linuxx8664gcc' + +# disable features +configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_DIR' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' + +moduleclass = 'data' -- GitLab From 29f76ad33050d5b831f116f64b79eb4dab79ef87 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 12 Jan 2015 13:52:07 +1300 Subject: [PATCH 006/722] New easyconfigs for GROMOS++ and gromosXX --- .../g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb | 30 +++++++++++++++++++ .../g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..1da3cc48d3 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'GROMOS++' +version = '1.0' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = ['%(namelower)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +sanity_check_paths = { + 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", + "lib/gromosplugin.a", "lib/libgromos.a"], + 'dirs': ["include", "share/gromos++"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..9b0643940a --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = ['%(name)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + #'files': ["bin/md", "bin/md_mpi"], + 'dirs': ['include/md++'], +} + +moduleclass = 'bio' -- GitLab From 744b58f10247ff8f494f6baa568b945b1eade69b Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 12 Jan 2015 16:37:06 +1300 Subject: [PATCH 007/722] Added support for a Linux group for restricting to licensed users --- easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb index 1da3cc48d3..557a5258d6 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb @@ -27,4 +27,5 @@ sanity_check_paths = { 'dirs': ["include", "share/gromos++"], } +group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb index 9b0643940a..428ee43e0b 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb @@ -27,4 +27,5 @@ sanity_check_paths = { 'dirs': ['include/md++'], } +group = 'gromos' moduleclass = 'bio' -- GitLab From bd538b2ddcdae6590ec32ba6297f94009b130ea2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 14 Jan 2015 14:09:44 +1300 Subject: [PATCH 008/722] Improved version numbering and OpenMP and MPI variants of GROMOS --- .../GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb | 36 +++++++++++++++++++ ... GROMOS++-1.0.2211-goolf-1.5.14-serial.eb} | 8 +++-- .../gromosXX-1.0.1737-goolf-1.5.14-mpi.eb | 36 +++++++++++++++++++ .../gromosXX-1.0.1737-goolf-1.5.14-openmp.eb | 36 +++++++++++++++++++ ... gromosXX-1.0.1737-goolf-1.5.14-serial.eb} | 8 +++-- 5 files changed, 120 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb rename easybuild/easyconfigs/g/GROMOS++/{GROMOS++-1.0-goolf-1.5.14.eb => GROMOS++-1.0.2211-goolf-1.5.14-serial.eb} (84%) create mode 100644 easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb create mode 100644 easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb rename easybuild/easyconfigs/g/gromosXX/{gromosXX-1.0-goolf-1.5.14.eb => gromosXX-1.0.1737-goolf-1.5.14-serial.eb} (83%) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb new file mode 100644 index 0000000000..f8faf80988 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'GROMOS++' +version = '1.0.2211' +versionsuffix = '-openmp' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': True, 'usempi': False} + +sources = ['%(namelower)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", + "lib/gromosplugin.a", "lib/libgromos.a"], + 'dirs': ["include", "share/gromos++"], +} + +group = 'gromos' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb similarity index 84% rename from easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb rename to easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb index 557a5258d6..31c8c80c13 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -6,7 +6,8 @@ easyblock = 'ConfigureMake' name = 'GROMOS++' -version = '1.0' +version = '1.0.2211' +versionsuffix = '-serial' homepage = 'http://www.gromos.net/' description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation @@ -16,11 +17,14 @@ Netherlands, and since then at the ETH, the Swiss Federal Institute of Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': False} -sources = ['%(namelower)s.tar.bz2'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] dependencies = [('GSL', '1.16')] +preconfigopts = './Config.sh &&' + sanity_check_paths = { 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", "lib/gromosplugin.a", "lib/libgromos.a"], diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb new file mode 100644 index 0000000000..1ca0239cec --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0.1737' +versionsuffix = '-mpi' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': True} + +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-mpi' + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + #'files': ["bin/md", "bin/md_mpi"], + 'dirs': ['include/md++'], +} + +group = 'gromos' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb new file mode 100644 index 0000000000..0845c8a493 --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0.1737' +versionsuffix = '-openmp' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': True, 'usempi': False} + +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + #'files': ["bin/md", "bin/md_mpi"], + 'dirs': ['include/md++'], +} + +group = 'gromos' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb similarity index 83% rename from easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb rename to easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb index 428ee43e0b..d48f6a0b1f 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -6,7 +6,8 @@ easyblock = 'ConfigureMake' name = 'gromosXX' -version = '1.0' +version = '1.0.1737' +versionsuffix = '-serial' homepage = 'http://www.gromos.net/' description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation @@ -16,11 +17,14 @@ Netherlands, and since then at the ETH, the Swiss Federal Institute of Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': False} -sources = ['%(name)s.tar.bz2'] +sources = ['%(name)s-%(version)s.tar.bz2'] dependencies = [('GSL', '1.16')] +preconfigopts = './Config.sh &&' + sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], #'files': ["bin/md", "bin/md_mpi"], -- GitLab From 750e44a9c09fafb64469a8e5a02000ded699cf85 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jan 2015 14:09:58 +1300 Subject: [PATCH 009/722] Updates as per comments --- .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb | 4 ++-- .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb | 4 ++-- .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb | 1 - 5 files changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb index f8faf80988..b0cbb9b351 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -19,7 +19,7 @@ Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'openmp': True, 'usempi': False} -sources = ['%(namelower)s-%(version)s.tar.bz2'] +sources = [SOURCELOWER_TAR_BZ2] dependencies = [('GSL', '1.16')] @@ -28,7 +28,7 @@ configopts = '--enable-openmp' sanity_check_paths = { 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", - "lib/gromosplugin.a", "lib/libgromos.a"], + "lib/gromosplugin.a", "lib/libgromos.a"], 'dirs': ["include", "share/gromos++"], } diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb index 31c8c80c13..9d4e1b8c63 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -19,7 +19,7 @@ Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'openmp': False, 'usempi': False} -sources = ['%(namelower)s-%(version)s.tar.bz2'] +sources = [SOURCELOWER_TAR_BZ2] dependencies = [('GSL', '1.16')] @@ -27,7 +27,7 @@ preconfigopts = './Config.sh &&' sanity_check_paths = { 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", - "lib/gromosplugin.a", "lib/libgromos.a"], + "lib/gromosplugin.a", "lib/libgromos.a"], 'dirs': ["include", "share/gromos++"], } diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb index 1ca0239cec..323c0f50ec 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -28,7 +28,6 @@ configopts = '--enable-mpi' sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], - #'files': ["bin/md", "bin/md_mpi"], 'dirs': ['include/md++'], } diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb index 0845c8a493..b47b02b824 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -28,7 +28,6 @@ configopts = '--enable-openmp' sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], - #'files': ["bin/md", "bin/md_mpi"], 'dirs': ['include/md++'], } diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb index d48f6a0b1f..d0b7ca517a 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -27,7 +27,6 @@ preconfigopts = './Config.sh &&' sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], - #'files': ["bin/md", "bin/md_mpi"], 'dirs': ['include/md++'], } -- GitLab From 873923b04ca2661d61be0993d2088332e2757f9f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 29 Jan 2015 10:51:00 +1300 Subject: [PATCH 010/722] Removed group directive per request from user @boegel --- .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb | 1 - .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb | 1 - .../easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb | 1 - 5 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb index b0cbb9b351..cd7029cdae 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -32,5 +32,4 @@ sanity_check_paths = { 'dirs': ["include", "share/gromos++"], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb index 9d4e1b8c63..2b1345c99b 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -31,5 +31,4 @@ sanity_check_paths = { 'dirs': ["include", "share/gromos++"], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb index 323c0f50ec..3020c00623 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -31,5 +31,4 @@ sanity_check_paths = { 'dirs': ['include/md++'], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb index b47b02b824..8cae45f338 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -31,5 +31,4 @@ sanity_check_paths = { 'dirs': ['include/md++'], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb index d0b7ca517a..075812f642 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -30,5 +30,4 @@ sanity_check_paths = { 'dirs': ['include/md++'], } -group = 'gromos' moduleclass = 'bio' -- GitLab From b7a9da861043eb87f6519823a05253022134e40e Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Thu, 26 Mar 2015 11:12:41 +1300 Subject: [PATCH 011/722] itac-9.0.3.051 --- .../easyconfigs/i/itac/itac-9.0.3.051.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb diff --git a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb new file mode 100644 index 0000000000..42551d67c6 --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb @@ -0,0 +1,21 @@ +name = 'itac' +version = '9.0.3.051' + +homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_itac_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +preferredmpi = 'impi5' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'tools' -- GitLab From 8febcc4dcee4b8aa71bb8b6315bae23de1ef8f6f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 29 Jul 2015 13:38:10 +1200 Subject: [PATCH 012/722] Added environment variable to force no CPU binding in Slurm --- easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb | 1 + 5 files changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index 76be1035a7..1082a356d5 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -30,3 +30,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb index 3b66a977f7..4fa5665414 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb @@ -31,3 +31,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb index c63048d89b..dc0616d42c 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb @@ -33,3 +33,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb index 5a28bbce0d..b2f34f7977 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb @@ -33,3 +33,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb index b63bd53de9..4c2e30db07 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb @@ -33,3 +33,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } -- GitLab From 29450f0d39654c8cf4ccaba1f97bab304e96d306 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 29 Jul 2015 15:57:32 +1200 Subject: [PATCH 013/722] ORCA 3.0.x is compiled against only OpenMPI 1.6.5 on linux --- ...nmpi_165.eb => ORCA-3_0_0-linux_x86-64.eb} | 6 ++-- .../ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb | 36 ------------------- ...PI-1.6.5.eb => ORCA-3_0_2-linux_x86-64.eb} | 6 ++-- ...PI-1.6.5.eb => ORCA-3_0_3-linux_x86-64.eb} | 6 ++-- 4 files changed, 7 insertions(+), 47 deletions(-) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_0-linux_x86-64_openmpi_165.eb => ORCA-3_0_0-linux_x86-64.eb} (90%) delete mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb => ORCA-3_0_2-linux_x86-64.eb} (91%) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb => ORCA-3_0_3-linux_x86-64.eb} (91%) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb similarity index 90% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb index 4fa5665414..1d969f2204 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb @@ -1,8 +1,7 @@ easyblock = "PackedBinary" name = "ORCA" -openmpiversion = '1.6.5' -version = '3_0_0-linux_x86-64_openmpi_%s' % ''.join(openmpiversion.split('.')) +version = '3_0_0-linux_x86-64' homepage = 'http://www.thch.uni-bonn.de/tc/orca/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry @@ -15,7 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] +# ORCA 3.0.0 is compiled only against OpenMPI 1.6.5 for Linux +dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb deleted file mode 100644 index b2f34f7977..0000000000 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = "PackedBinary" - -name = "ORCA" -version = '3_0_2-linux_x86-64' - -openmpiversion = '1.8.1' -versionsuffix = '-OpenMPI-%s' % openmpiversion - -homepage = 'http://cec.mpg.de/forum/' -description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry - with specific emphasis on spectroscopic properties of open-shell molecules. - It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- - and multireference correlated ab initio methods. - It can also treat environmental and relativistic effects.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] - -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.8.3')] - -sanity_check_paths = { - 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] - for y in ["", "_mpi"]] + \ - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', - 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ - ['orca', 'otool_cosmo'], - 'dirs': [], -} - -moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb similarity index 91% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb index dc0616d42c..39d6350aed 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -3,9 +3,6 @@ easyblock = "PackedBinary" name = "ORCA" version = '3_0_2-linux_x86-64' -openmpiversion = '1.6.5' -versionsuffix = '-OpenMPI-%s' % openmpiversion - homepage = 'http://cec.mpg.de/forum/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. @@ -17,7 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] +# ORCA 3.0.2 is compiled only against OpenMPI 1.6.5 for Linux +dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb similarity index 91% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb index 4c2e30db07..adeb3b2fac 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb @@ -3,9 +3,6 @@ easyblock = "PackedBinary" name = "ORCA" version = '3_0_3-linux_x86-64' -openmpiversion = '1.6.5' -versionsuffix = '-OpenMPI-%s' % openmpiversion - homepage = 'http://cec.mpg.de/forum/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. @@ -17,7 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] +# ORCA 3.0.3 is compiled only against OpenMPI 1.6.5 for Linux +dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', -- GitLab From 1d979ba9139bf6c729cc1e532614ce3e8723c564 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Sep 2015 15:14:08 +0300 Subject: [PATCH 014/722] Adding modified configs --- .../c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 12 ++++++------ .../easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb | 8 ++++---- .../{cp2k-2.4.0_ipi.patch => CP2K-2.4.0_ipi.patch} | 0 3 files changed, 10 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/c/CP2K/{cp2k-2.4.0_ipi.patch => CP2K-2.4.0_ipi.patch} (100%) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index 567f926654..b708ab38e5 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -12,18 +12,18 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://sourceforge.net/projects/cp2k/files/'] -sources = ['%s-%s.tar.bz2' % (name.lower(), version)] +sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'cp2k-2.4.0_ipi.patch', - 'fix_compile_date_lastcvs.patch', + 'CP2K-2.4.0_ipi.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', 'do_regtest_nocompile.patch' - ] +] builddependencies = [ ('flex', '2.5.35'), ('Bison', '2.5') - ] +] dependencies = [('Libint', '1.1.4')] @@ -34,4 +34,4 @@ parallel = 1 # about 100 tests fail ignore_regtest_fails=True -moduleclass = 'chem' + diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb index d44d72b4be..d3bcea99ca 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb @@ -11,17 +11,17 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://sourceforge.net/projects/cp2k/files/'] -sources = ['%s-%s.tar.bz2' % (name.lower(), version)] +sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'fix_compile_date_lastcvs.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', 'do_regtest_nocompile.patch' - ] +] builddependencies = [ ('flex', '2.5.35'), ('Bison', '2.5') - ] +] dependencies = [('Libint', '1.1.4')] diff --git a/easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch similarity index 100% rename from easybuild/easyconfigs/c/CP2K/cp2k-2.4.0_ipi.patch rename to easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch -- GitLab From 3e1f8943e1ff8924bee86a1ca13c0b4527d18352 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Sep 2015 15:16:30 +0300 Subject: [PATCH 015/722] last changes --- .../easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 2 +- .../easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch | 11 ----------- 2 files changed, 1 insertion(+), 12 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index b708ab38e5..aa550ff0b9 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -34,4 +34,4 @@ parallel = 1 # about 100 tests fail ignore_regtest_fails=True - +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch deleted file mode 100644 index a50d6e9cf4..0000000000 --- a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- makefiles/Makefile.orig 2012-08-21 14:35:17.000000000 +0300 -+++ makefiles/Makefile 2013-11-12 12:41:29.361582641 +0200 -@@ -194,7 +194,7 @@ - # - ifeq ($(CPPSHELL),) - CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ -- -D__COMPILE_DATE="\"$(shell date)\""\ -+ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g')\""\ - -D__COMPILE_HOST="\"$(shell hostname)\""\ - -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" - endif -- GitLab From e61aac2fab0c11ba2dda71871b89e71c2e632e60 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Sep 2015 16:04:42 +0300 Subject: [PATCH 016/722] Adding accidentally deleted patch --- .../easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch new file mode 100644 index 0000000000..a50d6e9cf4 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch @@ -0,0 +1,11 @@ +--- makefiles/Makefile.orig 2012-08-21 14:35:17.000000000 +0300 ++++ makefiles/Makefile 2013-11-12 12:41:29.361582641 +0200 +@@ -194,7 +194,7 @@ + # + ifeq ($(CPPSHELL),) + CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ +- -D__COMPILE_DATE="\"$(shell date)\""\ ++ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g')\""\ + -D__COMPILE_HOST="\"$(shell hostname)\""\ + -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" + endif -- GitLab From 6dfa12bbcd946d3eab429cf96037dc8fcb6ced3b Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 22 Sep 2015 15:06:43 +0300 Subject: [PATCH 017/722] Making changes according to comments --- .../easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 6 +++--- .../easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch | 2 ++ .../easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch | 11 ----------- 4 files changed, 6 insertions(+), 15 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index aa550ff0b9..5716e9f33a 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -15,8 +15,8 @@ source_urls = ['http://sourceforge.net/projects/cp2k/files/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'CP2K-2.4.0_ipi.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', + 'CP2K-%(version)s_ipi.patch', + 'CP2K-%(version)s-fix_compile_date_lastsvn.patch', 'do_regtest_nocompile.patch' ] @@ -34,4 +34,4 @@ parallel = 1 # about 100 tests fail ignore_regtest_fails=True -moduleclass = 'chem' + diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb index d3bcea99ca..5c6f21e195 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb @@ -14,7 +14,7 @@ source_urls = ['http://sourceforge.net/projects/cp2k/files/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', + 'CP2K-%(version)s-fix_compile_date_lastsvn.patch', 'do_regtest_nocompile.patch' ] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch index b8115df6c5..3c7cc4aaec 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0_ipi.patch @@ -1,4 +1,6 @@ #This patch makes CP2K source code compatible with i-pi +#It was created by the CP2K team and can be found in the following link: +#https://github.com/i-pi/i-pi/tree/master/patches diff -rupN cp2k-2.4.0_ref/makefiles/Makefile cp2k-2.4.0/makefiles/Makefile --- cp2k-2.4.0_ref/makefiles/Makefile 2013-08-15 10:46:04.535899216 +0100 +++ cp2k-2.4.0/makefiles/Makefile 2013-08-15 10:53:45.827911028 +0100 diff --git a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch deleted file mode 100644 index a50d6e9cf4..0000000000 --- a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- makefiles/Makefile.orig 2012-08-21 14:35:17.000000000 +0300 -+++ makefiles/Makefile 2013-11-12 12:41:29.361582641 +0200 -@@ -194,7 +194,7 @@ - # - ifeq ($(CPPSHELL),) - CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ -- -D__COMPILE_DATE="\"$(shell date)\""\ -+ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g')\""\ - -D__COMPILE_HOST="\"$(shell hostname)\""\ - -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" - endif -- GitLab From 1c99c6b8f1c70ce1f5d6bd21d959ef4c592ece44 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 22 Sep 2015 15:31:55 +0300 Subject: [PATCH 018/722] adding back original patch file --- .../c/CP2K/fix_compile_date_lastcvs.patch | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch new file mode 100644 index 0000000000..97dca5d868 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastcvs.patch @@ -0,0 +1,14 @@ +--- makefiles/Makefile.orig 2010-12-10 05:35:15.000000000 +0100 ++++ makefiles/Makefile 2011-01-24 10:14:35.000000000 +0100 +@@ -149,9 +149,9 @@ + # + ifeq ($(CPPSHELL),) + CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ +- -D__COMPILE_DATE="\"$(shell date)\""\ ++ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g')\""\ + -D__COMPILE_HOST="\"$(shell hostname)\""\ +- -D__COMPILE_LASTCVS="\"$(shell tail -n1 $(SRCDIR)/CVS/Entries)\"" ++ -D__COMPILE_LASTCVS="\"$(shell tail -n1 $(SRCDIR)/CVS/Entries | sed 's/ /_/g')\"" + endif + + ifneq ($(CPP),) -- GitLab From 362a6d3cb7afa719253aafe12c3aeb8a8cfe88ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 14:56:37 +0200 Subject: [PATCH 019/722] remove old svnversion build dep in Python 2.5.6 easyconfigs (patch makes it uneccesary) --- .../p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 4 ---- .../p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 4 ---- .../easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 4 ---- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 4 ---- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 4 ---- .../easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 4 ---- .../easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 4 ---- 7 files changed, 28 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index 7756ecc5cf..43ff3feba7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -21,10 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index 6f7b7074bb..f825fd87bd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -21,10 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index 2b86e4f482..18d0d4a8df 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -21,10 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index ad5a259b72..23ddabe854 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -24,10 +24,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index 061722f46e..f747214b5c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -24,10 +24,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index cfb317b18e..0228eae5be 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -21,10 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index ad8051da17..fc44c37e78 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -21,10 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -# Python 2.5 requires an old subversion version to build correctly, -# in which 'svnversion' returns 'exported' rather than 'Unversioned directory' -builddependencies = [('subversion', '1.6.23')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' -- GitLab From 29cf2032b0d98eaa677c83aa38f5907f600c570d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 16:42:32 +0200 Subject: [PATCH 020/722] fix conflict --- .../l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb index f473597909..96f39c944c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -4,13 +4,8 @@ name = 'libxml2' version = '2.9.1' homepage = 'http://xmlsoft.org/' -<<<<<<< HEAD -description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable -outside of the Gnome platform).""" -======= description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" ->>>>>>> develop toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -- GitLab From 05cfc4122c9ea2ddcd7c5502bb5bad82ed9708c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 16:46:30 +0200 Subject: [PATCH 021/722] trash easyconfigs with different toolchains, stick to just goolf/1.4.10 --- .../APR-util-1.5.3-goalf-1.1.0-no-OFED.eb | 23 ------------ .../APR-util-1.5.3-gompi-1.4.12-no-OFED.eb | 23 ------------ .../a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb | 23 ------------ .../a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb | 23 ------------ .../a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb | 23 ------------ .../a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb | 23 ------------ .../a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb | 17 --------- .../a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb | 17 --------- .../a/APR/APR-1.5.0-ictce-4.0.6.eb | 17 --------- .../a/APR/APR-1.5.0-ictce-4.1.13.eb | 17 --------- .../a/APR/APR-1.5.0-ictce-5.2.0.eb | 17 --------- .../a/APR/APR-1.5.0-ictce-5.3.0.eb | 17 --------- .../n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb | 24 ------------- .../neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb | 24 ------------- .../n/neon/neon-0.30.0-ictce-4.0.6.eb | 24 ------------- .../n/neon/neon-0.30.0-ictce-4.1.13.eb | 24 ------------- .../n/neon/neon-0.30.0-ictce-5.2.0.eb | 24 ------------- .../n/neon/neon-0.30.0-ictce-5.3.0.eb | 24 ------------- .../Python-2.5.6-gompi-1.5.12-no-OFED-bare.eb | 26 -------------- .../SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb | 35 ------------------- .../SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb | 35 ------------------- .../s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb | 35 ------------------- .../s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb | 35 ------------------- .../s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb | 35 ------------------- .../s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb | 35 ------------------- .../subversion-1.6.23-goalf-1.1.0-no-OFED.eb | 28 --------------- .../subversion-1.6.23-gompi-1.4.12-no-OFED.eb | 28 --------------- .../subversion-1.6.23-ictce-4.0.6.eb | 28 --------------- .../subversion-1.6.23-ictce-4.1.13.eb | 28 --------------- .../subversion-1.6.23-ictce-5.2.0.eb | 28 --------------- .../subversion-1.6.23-ictce-5.3.0.eb | 28 --------------- .../subversion-1.8.8-ictce-4.1.13.eb | 28 --------------- .../t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb | 19 ---------- .../t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb | 19 ---------- .../t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb | 19 ---------- .../t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb | 19 ---------- .../t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb | 19 ---------- 37 files changed, 911 deletions(-) delete mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb delete mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb delete mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb delete mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb delete mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb delete mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb delete mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb delete mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb delete mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb delete mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb delete mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb delete mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb delete mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb delete mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb delete mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb delete mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb delete mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb delete mode 100644 easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.5.12-no-OFED-bare.eb delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb delete mode 100755 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb delete mode 100755 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb delete mode 100755 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index f2b2f6d4d4..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index f5f429b778..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb deleted file mode 100644 index 6785705751..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.0.6.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb deleted file mode 100644 index ab0ac9c226..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-4.1.13.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb deleted file mode 100644 index 669555d663..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.2.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb deleted file mode 100644 index 5820665193..0000000000 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-ictce-5.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'APR-util' -version = '1.5.3' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) util libraries." - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('APR', '1.5.0')] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config" - -sanity_check_paths = { - 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], - 'dirs': ["include/apr-1"], -} - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index 42d75b76df..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index c9b38d32bc..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb deleted file mode 100644 index bb13d21a33..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.0.6.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb deleted file mode 100644 index c26ce2075a..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-4.1.13.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb deleted file mode 100644 index 3f74bca0b9..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.2.0.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb deleted file mode 100644 index 7c6b787d78..0000000000 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-ictce-5.3.0.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'APR' -version = '1.5.0' - -homepage = 'http://apr.apache.org/' -description = "Apache Portable Runtime (APR) libraries." - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = ['http://archive.apache.org/dist/apr/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], - 'dirs': ["include/apr-1"], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index f111e9310e..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index 212229e999..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb deleted file mode 100644 index fdf1eabe1a..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.0.6.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb deleted file mode 100644 index 97eea6a566..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-4.1.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb deleted file mode 100644 index 244a91df81..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.2.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb deleted file mode 100644 index 6dd467a1fe..0000000000 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-ictce-5.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'neon' -version = '0.30.0' - -homepage = 'http://www.webdav.org/neon/' -description = "neon is an HTTP and WebDAV client library, with a C interface." - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = [homepage] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.7'), - ('libxml2', '2.9.1'), -] - -configopts = "--with-libxml2" - -sanity_check_paths = { - 'files': ["bin/neon-config", "lib/libneon.a"], - 'dirs': ["include/neon"], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.5.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.5.12-no-OFED-bare.eb deleted file mode 100644 index fbb6fb607f..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.5.12-no-OFED-bare.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'Python' -version = '2.5.6' -versionsuffix = '-bare' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -patches = ['Python-%(version)s_svnversion-cmd.patch'] - -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.7'), - ('libreadline', '6.2'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index 1f9d380786..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index 330ea91aef..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb deleted file mode 100644 index 8ab8985748..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.0.6.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb deleted file mode 100644 index 6948614b01..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-4.1.13.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb deleted file mode 100644 index 6a16570c53..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.2.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb deleted file mode 100644 index 499e33114e..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-ictce-5.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -name = 'SQLite' -version = '3.8.4.1' - -homepage = 'http://www.hwaci.com/sw/sqlite/' -description = "SQLite: SQL Database Engine in a C Library" - -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -dependencies = [ - ('libreadline', '6.2'), - ('Tcl', '8.6.1'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index 10fcdfa9b8..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index 18b01448ee..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb deleted file mode 100644 index cc7766f42b..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.0.6.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb deleted file mode 100644 index 0e7556d3dd..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-4.1.13.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb deleted file mode 100644 index 3dd8117f6f..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.2.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb deleted file mode 100644 index 8b59c05878..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-ictce-5.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.6.23' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb deleted file mode 100644 index 672480bf95..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-ictce-4.1.13.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.8.8' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index 688b7db304..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Tcl' -version = '8.6.1' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb deleted file mode 100644 index bf05390914..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-gompi-1.4.12-no-OFED.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Tcl' -version = '8.6.1' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb deleted file mode 100755 index 4497a53f78..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.0.6.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Tcl' -version = '8.6.1' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb deleted file mode 100755 index a112f672e2..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-4.1.13.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Tcl' -version = '8.6.1' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb deleted file mode 100755 index d9d3d41205..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.2.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Tcl' -version = '8.6.1' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'ictce', 'version': '5.2.0'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' -- GitLab From 173a810ac34382286a46d66d706adab97a9bcf49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 16:48:49 +0200 Subject: [PATCH 022/722] add missing 'easyblock' line --- .../a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb | 2 ++ .../easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb | 2 ++ .../easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb | 2 ++ .../s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb | 1 + .../s/subversion/subversion-1.6.23-goolf-1.4.10.eb | 12 +++++++----- 5 files changed, 14 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb index f2b44bb9a1..1a3a23018b 100644 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.3-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'APR-util' version = '1.5.3' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb index e069e515a2..bbe4a3f6c2 100644 --- a/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/APR/APR-1.5.0-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'APR' version = '1.5.0' diff --git a/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb b/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb index dbf0e6619b..2732f2ab74 100644 --- a/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/neon/neon-0.30.0-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'neon' version = '0.30.0' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb index 72c8d21c52..5d1c89464a 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb @@ -9,6 +9,7 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/ ## +easyblock = 'ConfigureMake' name = 'SQLite' version = '3.8.4.1' diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb index c4f4b6ed90..e53ac64a5b 100644 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'subversion' version = '1.6.23' @@ -9,11 +11,6 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://archive.apache.org/dist/subversion/'] sources = [SOURCE_TAR_GZ] -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - dependencies = [ ('APR', '1.5.0'), ('APR-util', '1.5.3'), @@ -25,4 +22,9 @@ dependencies = [ configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + moduleclass = 'tools' -- GitLab From 7b78413357e94593a19d8b7e13dca2ac90077da1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 16:51:21 +0200 Subject: [PATCH 023/722] remove easyconfig for subversion 1.8.8 (see #1970) --- .../subversion-1.8.8-goolf-1.4.10.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb b/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb deleted file mode 100644 index 5f9488ba6c..0000000000 --- a/easybuild/easyconfigs/s/subversion/subversion-1.8.8-goolf-1.4.10.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'subversion' -version = '1.8.8' - -homepage = 'http://subversion.apache.org/' -description = " Subversion is an open source version control system." - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ["bin/svn", "bin/svnversion"], - 'dirs': [], -} - -dependencies = [ - ('APR', '1.5.0'), - ('APR-util', '1.5.3'), - ('SQLite', '3.8.4.1'), - ('zlib', '1.2.7'), - ('neon', '0.30.0'), -] - -configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -configopts += "--with-zlib=$EBROOTZLIB --with-neon=$EBROOTNEON" - -moduleclass = 'tools' -- GitLab From 067f1e9ebdab00845652acaaa2f562358e9d279d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 16:52:24 +0200 Subject: [PATCH 024/722] trash extra libxml2 easyconfig --- ...libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100755 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb deleted file mode 100755 index d68ae2eaee..0000000000 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'libxml2' -version = '2.9.1' - -homepage = 'http://xmlsoft.org/' -description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable - outside of the Gnome platform).""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] - -configopts = 'CC="$CC" CXX="$CXX" --with-pic' - -pythonver = '2.7.5' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - -dependencies = [ - ('zlib', '1.2.8'), - ('Python', pythonver), -] - -moduleclass = 'lib' -- GitLab From 08257022563059a4d3c0c1134a8ce44174015542 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 18:40:14 +0200 Subject: [PATCH 025/722] subversion -> Subversion --- .../Subversion-1.6.23-goolf-1.4.10.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/{subversion/subversion-1.6.23-goolf-1.4.10.eb => Subversion/Subversion-1.6.23-goolf-1.4.10.eb} (97%) diff --git a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb similarity index 97% rename from easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb rename to easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb index e53ac64a5b..fc1179c894 100644 --- a/easybuild/easyconfigs/s/subversion/subversion-1.6.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'subversion' +name = 'Subversion' version = '1.6.23' homepage = 'http://subversion.apache.org/' -- GitLab From ea7c25c2cb7c2dcd8b20623199891abf407712ab Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 23 Sep 2015 10:35:34 +0300 Subject: [PATCH 026/722] Adding moduleclass --- easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index 5716e9f33a..7188e62917 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -34,4 +34,4 @@ parallel = 1 # about 100 tests fail ignore_regtest_fails=True - +moduleclass = 'chem' -- GitLab From 98d4e2d24f4a8dab9c9b5dfd0edf58ea60d6e240 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 12:03:12 +0200 Subject: [PATCH 027/722] fix sources spec --- .../easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb index fc1179c894..07b1072638 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.6.23-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = " Subversion is an open source version control system." toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://archive.apache.org/dist/subversion/'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('APR', '1.5.0'), -- GitLab From 9f185b43cf9bf44d3d34cc79627508acff8a92d3 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 30 Oct 2015 12:38:28 +1300 Subject: [PATCH 028/722] New easyconfig for DFT-D3 --- .../d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb new file mode 100644 index 0000000000..b28f706ce6 --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.1.1' + +homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] +sources = ['dftd3.tgz'] + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 339843c8214e538e3e4504fa272cf25d44f2db1f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 2 Nov 2015 11:22:04 +1300 Subject: [PATCH 029/722] Added MD5 checksum for tarball --- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index b28f706ce6..79b12d07a2 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] sources = ['dftd3.tgz'] +checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From 57f73ac1adc543a5a4e1e378bf2c6703eefa2728 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 6 Jan 2016 13:25:32 +1300 Subject: [PATCH 030/722] Comment out checksum, rename source file and add an explanatory comment --- .../easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 79b12d07a2..54c92da4c6 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -9,8 +9,13 @@ description = """DFT-D3 implements a dispersion correction for density functiona toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] -sources = ['dftd3.tgz'] -checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] +# Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version +# numbering. Also, the authors are prone (alas) to stealth upgrades, so that two +# tarballs with the same version number can have different checksums. For this +# reason, it is suggested to manually download and rename the tarball, and the +# checksum input has been disabled. +sources = ['dftd3-%(version)s.tgz'] +#checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From a5965e7a9e0133e17be5fbc26bfa677b98690222 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 26 Jan 2016 10:46:13 +1300 Subject: [PATCH 031/722] Re-enable checksum verification --- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 54c92da4c6..3ea34a9824 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -12,10 +12,10 @@ source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] # Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version # numbering. Also, the authors are prone (alas) to stealth upgrades, so that two # tarballs with the same version number can have different checksums. For this -# reason, it is suggested to manually download and rename the tarball, and the -# checksum input has been disabled. +# reason, it is suggested to manually download and rename the tarball. The +# checksum may also need updating from time to time. sources = ['dftd3-%(version)s.tgz'] -#checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] +checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From d20fd461af0643a43a7e80b8cc740aa480f45276 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:18:16 +1300 Subject: [PATCH 032/722] New EasyConfig for GDAL 2.0.1 with the foss-2015a toolchain --- .../g/GDAL/GDAL-2.0.1-foss-2015a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb new file mode 100644 index 0000000000..fdbd875ff2 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.1' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('KEALib', '1.4.4'), + ('netCDF', '4.3.3.1'), + ('HDF5', '1.8.16'), + ('expat', '2.1.0'), + ('libxml2', '2.9.3', '-Python-2.7.11'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' -- GitLab From fa11863cf5cb4aa57b73db4336ac0d2cae1b0504 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:20:50 +1300 Subject: [PATCH 033/722] New EasyConfigs for libspatialite - various versions and toolchains --- .../libspatialite-4.1.1-goolf-1.5.14.eb | 27 ++++++++++++++++ .../libspatialite-4.3.0-intel-2015a.eb | 32 +++++++++++++++++++ .../libspatialite-4.3.0a-foss-2015a.eb | 32 +++++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..8132d40673 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.1.1' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +patches = ['libspatialite-configure.ac.patch'] + +dependencies = [('FreeXL','1.0.0g'),('GEOS','3.3.5'), ('SQLite', '3.8.4.3'), ('PROJ', '4.8.0')] +configopts = '--disable-geosadvanced' +builddependencies = [('CMake', '2.8.10.2')] + +sanity_check_paths = { + 'files': ["lib/libspatialite.la"], + 'dirs': ["lib","include"] + } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb new file mode 100644 index 0000000000..732c224f99 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.3.0' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('FreeXL','1.0.1'), + ('GEOS','3.3.9'), + ('SQLite', '3.8.9'), + ('PROJ', '4.9.1'), +] + +configopts = '--disable-geosadvanced' + +builddependencies = [('CMake', '3.2.2')] + +sanity_check_paths = { + 'files': ["lib/libspatialite.la"], + 'dirs': ["lib","include"] + } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb new file mode 100644 index 0000000000..0c50d9148b --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.3.0a' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('FreeXL', '1.0.2'), + ('GEOS', '3.5.0', '-Python-2.7.11'), + ('SQLite', '3.10.0'), + ('PROJ', '4.9.1'), +] + +configopts = '--disable-geosadvanced' + +builddependencies = [('CMake', '3.4.1')] + +sanity_check_paths = { + 'files': ["lib/libspatialite.la"], + 'dirs': ["lib","include"] + } + +moduleclass = 'lib' -- GitLab From cdf12d46eff5743af67cf80615ac0800ce10c11a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 16 Feb 2016 12:08:41 +1300 Subject: [PATCH 034/722] Add RSH_COMMAND variable to module files for ORCA --- easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb | 6 +++++- easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb | 6 +++++- easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb | 6 +++++- easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb | 6 +++++- 4 files changed, 20 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index 1082a356d5..1f68602fad 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -29,5 +29,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb index 1d969f2204..976f97b5d5 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb @@ -30,5 +30,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb index 39d6350aed..e21c8f3ed4 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -30,5 +30,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb index adeb3b2fac..547be86ff0 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb @@ -30,5 +30,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } -- GitLab From 829d4bce5aa38d6444c4eb516969f6264205b4d3 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 18 Feb 2016 13:33:41 +1300 Subject: [PATCH 035/722] Reinstate Open MPI version --- easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb index bd3a091b31..9110e61a28 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb @@ -1,7 +1,8 @@ easyblock = "PackedBinary" name = "ORCA" -version = '3_0_0-linux_x86-64' +openmpiversion = '1.6.5' +version = '3_0_0-linux_x86-64_openmpi_%s' % ''.join(openmpiversion.split('.')) homepage = 'http://www.thch.uni-bonn.de/tc/orca/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry @@ -15,7 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] # ORCA 3.0.0 is compiled only against OpenMPI 1.6.5 for Linux -dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] +dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', -- GitLab From 0496a6bd9d329ae1748ca82b211a7a63380dd151 Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 18 Feb 2016 17:10:39 +0200 Subject: [PATCH 036/722] add easyconfig Boost-1.59.0-intel-2015b.eb --- .../b/Boost/Boost-1.59.0-intel-2015b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb new file mode 100644 index 0000000000..7461992321 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.59.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 8ad5823fa146d339ad0d9bd4b5e6f4f3a1eeb7b0 Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 18 Feb 2016 17:11:56 +0200 Subject: [PATCH 037/722] add easyconfig OpenFOAM-3.0.0-intel-2015b.eb --- .../o/OpenFOAM/OpenFOAM-3.0.0-intel-2015b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-intel-2015b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-intel-2015b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-intel-2015b.eb new file mode 100644 index 0000000000..eb8704d554 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-intel-2015b.eb @@ -0,0 +1,40 @@ +name = 'OpenFOAM' +version = '3.0.0' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'cstd': 'c++14'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-%(version)s_libreadline.patch', + ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0', '-32bitIDX'), + ('ncurses', '5.9'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.59.0'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.3.2'), + ('flex', '2.5.39'), +] + +moduleclass = 'cae' -- GitLab From c08bd4a87dc921af2bf10fe29a6f8a604787ddeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 20:19:42 +0100 Subject: [PATCH 038/722] {toolchain}[dummy] intel 2016.02 --- .../easyconfigs/i/intel/intel-2016.02.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel/intel-2016.02.eb diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02.eb b/easybuild/easyconfigs/i/intel/intel-2016.02.eb new file mode 100644 index 0000000000..4c2ff105d6 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.02.eb @@ -0,0 +1,25 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'intel' +version = '2016.02' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.2.181' +gccver = '4.9.3' +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.2.181', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' -- GitLab From 3807a518db8659408f9261906b69c3a819a3b98f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 20:55:57 +0100 Subject: [PATCH 039/722] bump GCC to 5.3.0 --- easybuild/easyconfigs/i/intel/intel-2016.02.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02.eb b/easybuild/easyconfigs/i/intel/intel-2016.02.eb index 4c2ff105d6..47932a57f9 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02.eb @@ -10,7 +10,7 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.2.181' -gccver = '4.9.3' +gccver = '5.3.0' binutilsver = '2.26' gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ -- GitLab From 0907ea3fd1c6bbeaeb6064ba47eddb79851b6551 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 23:12:00 +0100 Subject: [PATCH 040/722] {compiler}[dummp] GCC 5.3.0-2.26 --- .../b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb | 27 + .../b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 41 + .../easyconfigs/b/binutils/binutils-2.26.eb | 39 + .../f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 16 + easybuild/easyconfigs/f/flex/flex-2.6.0.eb | 16 + easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb | 25 + .../easyconfigs/g/GCCcore/GCCcore-4.9.3.eb | 3 +- .../easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 54 + .../mpfr-3.1.3-allpatches-20151029.patch | 1830 +++++++++++++++++ .../m/M4/M4-1.4.17-GCCcore-5.3.0.eb | 26 + .../z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb | 25 + 11 files changed, 2100 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..b7cebec049 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.26', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..ca71c5f04e --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb new file mode 100644 index 0000000000..5145e1becd --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), +] + +# statically link with zlib, to avoid runtime dependency on zlib +# further, add the system library path in the rpath: this should 'harden' the +# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' +prebuildopts = preconfigopts + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..f20e1d0126 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb new file mode 100644 index 0000000000..e7580df4ae --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..34bf1f36a8 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '5.3.0' + +binutilsver = '2.26' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index 268b052687..40449db3d5 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -10,7 +10,6 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' -gcc_name = 'GCC' source_urls = [ 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror @@ -19,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ - '%s-%s.tar.bz2' % (gcc_name.lower(), version), + 'gcc-%(version)s.tar.bz2', 'gmp-6.0.0a.tar.bz2', 'mpfr-%s.tar.gz' % mpfr_version, 'mpc-1.0.2.tar.gz', diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb new file mode 100644 index 0000000000..e7aac86863 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '5.3.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.3' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.0.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.15.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20151029.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [ + ('binutils', '2.26'), + ('M4', '1.4.17'), +] + +checksums = [ + 'c9616fd448f980259c31de613e575719', # gcc-5.3.0.tar.bz2 + '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 + '7b650781f0a7c4a62e9bc8bdaaa0018b', # mpfr-3.1.3.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + '8428efbbc6f6e2810ce5c1ba73ecf98c', # isl-0.15.tar.bz2 + '6476b450c3db177b2250f3549362380e', # mpfr-3.1.3-allpatches-20151029.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch new file mode 100644 index 0000000000..891831f521 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch @@ -0,0 +1,1830 @@ +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:49:23.950112879 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:49:24.042113845 +0000 +@@ -0,0 +1 @@ ++lngamma-and-doc +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-06-19 19:55:09.000000000 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:49:24.042113845 +0000 +@@ -1 +1 @@ +-3.1.3 ++3.1.3-p1 +diff -Naurd mpfr-3.1.3-a/doc/mpfr.texi mpfr-3.1.3-b/doc/mpfr.texi +--- mpfr-3.1.3-a/doc/mpfr.texi 2015-06-19 19:55:11.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.texi 2015-07-02 10:49:24.018113593 +0000 +@@ -810,13 +810,17 @@ + When the input point is in the closure of the domain of the mathematical + function and an input argument is +0 (resp.@: @minus{}0), one considers + the limit when the corresponding argument approaches 0 from above +-(resp.@: below). If the limit is not defined (e.g., @code{mpfr_log} on +-@minus{}0), the behavior is specified in the description of the MPFR function. ++(resp.@: below), if possible. If the limit is not defined (e.g., ++@code{mpfr_sqrt} and @code{mpfr_log} on @minus{}0), the behavior is ++specified in the description of the MPFR function, but must be consistent ++with the rule from the above paragraph (e.g., @code{mpfr_log} on @pom{}0 ++gives @minus{}Inf). + + When the result is equal to 0, its sign is determined by considering the + limit as if the input point were not in the domain: If one approaches 0 + from above (resp.@: below), the result is +0 (resp.@: @minus{}0); +-for example, @code{mpfr_sin} on +0 gives +0. ++for example, @code{mpfr_sin} on @minus{}0 gives @minus{}0 and ++@code{mpfr_acos} on 1 gives +0 (in all rounding modes). + In the other cases, the sign is specified in the description of the MPFR + function; for example @code{mpfr_max} on @minus{}0 and +0 gives +0. + +@@ -832,8 +836,8 @@ + @c that advantages in practice), like for any bug fix. + Example: @code{mpfr_hypot} on (NaN,0) gives NaN, but @code{mpfr_hypot} + on (NaN,+Inf) gives +Inf (as specified in @ref{Special Functions}), +-since for any finite input @var{x}, @code{mpfr_hypot} on (@var{x},+Inf) +-gives +Inf. ++since for any finite or infinite input @var{x}, @code{mpfr_hypot} on ++(@var{x},+Inf) gives +Inf. + + @node Exceptions, Memory Handling, Floating-Point Values on Special Numbers, MPFR Basics + @comment node-name, next, previous, up +@@ -1581,7 +1585,8 @@ + @deftypefunx int mpfr_add_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_add_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} + @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) + 0 = (+0) and (@minus{}0) + 0 = (@minus{}0)). + The @code{mpfr_add_d} function assumes that the radix of the @code{double} type + is a power of 2, with a precision at most that declared by the C implementation +@@ -1599,7 +1604,8 @@ + @deftypefunx int mpfr_sub_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sub_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} - @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) @minus{} 0 = (+0), (@minus{}0) @minus{} 0 = (@minus{}0), + 0 @minus{} (+0) = (@minus{}0) and 0 @minus{} (@minus{}0) = (+0)). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_sub} +@@ -1615,7 +1621,7 @@ + Set @var{rop} to @math{@var{op1} @GMPtimes{} @var{op2}} rounded in the + direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_mul_d}. + @end deftypefun + +@@ -1635,7 +1641,7 @@ + @deftypefunx int mpfr_div_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1}/@var{op2}} rounded in the direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_div} + and @code{mpfr_div_d}. + @end deftypefun +@@ -1643,15 +1649,18 @@ + @deftypefun int mpfr_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sqrt_ui (mpfr_t @var{rop}, unsigned long int @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{\sqrt{@var{op}}, the square root of @var{op}} +-rounded in the direction @var{rnd} (set @var{rop} to @minus{}0 if @var{op} is +-@minus{}0, to be consistent with the IEEE 754 standard). ++rounded in the direction @var{rnd}. Set @var{rop} to @minus{}0 if ++@var{op} is @minus{}0, to be consistent with the IEEE 754 standard. + Set @var{rop} to NaN if @var{op} is negative. + @end deftypefun + + @deftypefun int mpfr_rec_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{1/\sqrt{@var{op}}, the reciprocal square root of @var{op}} +-rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is +-@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. ++rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is ++@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. Warning! ++Therefore the result on @minus{}0 is different from the one of the rSqrt ++function recommended by the IEEE 754-2008 standard (Section 9.2.1), which ++is @minus{}Inf instead of +Inf. + @end deftypefun + + @deftypefun int mpfr_cbrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -1832,7 +1841,9 @@ + @m{\log_2 @var{op}, log2(@var{op})} or + @m{\log_{10} @var{op}, log10(@var{op})}, respectively, + rounded in the direction @var{rnd}. +-Set @var{rop} to @minus{}Inf if @var{op} is @minus{}0 ++Set @var{rop} to +0 if @var{op} is 1 (in all rounding modes), ++for consistency with the ISO C99 and IEEE 754-2008 standards. ++Set @var{rop} to @minus{}Inf if @var{op} is @pom{}0 + (i.e., the sign of the zero has no influence on the result). + @end deftypefun + +@@ -2003,8 +2014,11 @@ + @deftypefun int mpfr_lngamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to the value of the logarithm of the Gamma function on @var{op}, + rounded in the direction @var{rnd}. +-When @math{@minus{}2@var{k}@minus{}1 @le{} @var{op} @le{} @minus{}2@var{k}}, +-@var{k} being a non-negative integer, @var{rop} is set to NaN. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf, ++following the general rules on special values. ++When @math{@minus{}2@var{k}@minus{}1 < @var{op} < @minus{}2@var{k}}, ++@var{k} being a nonnegative integer, set @var{rop} to NaN@. + See also @code{mpfr_lgamma}. + @end deftypefun + +@@ -2012,10 +2026,11 @@ + Set @var{rop} to the value of the logarithm of the absolute value of the + Gamma function on @var{op}, rounded in the direction @var{rnd}. The sign + (1 or @minus{}1) of Gamma(@var{op}) is returned in the object pointed to +-by @var{signp}. When @var{op} is an infinity or a non-positive integer, set +-@var{rop} to +Inf. When @var{op} is NaN, @minus{}Inf or a negative integer, +-*@var{signp} is undefined, and when @var{op} is @pom{}0, *@var{signp} is +-the sign of the zero. ++by @var{signp}. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf. ++When @var{op} is NaN, @minus{}Inf or a negative integer, *@var{signp} is ++undefined, and when @var{op} is @pom{}0, *@var{signp} is the sign of the zero. + @end deftypefun + + @deftypefun int mpfr_digamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -2064,7 +2079,10 @@ + @deftypefunx int mpfr_fms (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_t @var{op3}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{(@var{op1} @GMPtimes{} @var{op2}) + @var{op3}} + (resp.@: @math{(@var{op1} @GMPtimes{} @var{op2}) - @var{op3}}) +-rounded in the direction @var{rnd}. ++rounded in the direction @var{rnd}. Concerning special values (signed zeros, ++infinities, NaN), these functions behave like a multiplication followed by a ++separate addition or subtraction. That is, the fused operation matters only ++for rounding. + @end deftypefun + + @deftypefun int mpfr_agm (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_rnd_t @var{rnd}) +@@ -2089,8 +2107,8 @@ + i.e., $\sqrt{x^2+y^2}$, + @end tex + rounded in the direction @var{rnd}. +-Special values are handled as described in Section F.9.4.3 of +-the ISO C99 and IEEE 754-2008 standards: ++Special values are handled as described in the ISO C99 (Section F.9.4.3) ++and IEEE 754-2008 (Section 9.2.1) standards: + If @var{x} or @var{y} is an infinity, then +Inf is returned in @var{rop}, + even if the other number is NaN. + @end deftypefun +diff -Naurd mpfr-3.1.3-a/doc/mpfr.info mpfr-3.1.3-b/doc/mpfr.info +--- mpfr-3.1.3-a/doc/mpfr.info 2015-06-19 19:55:53.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.info 2015-07-02 10:49:38.718267817 +0000 +@@ -1,4 +1,4 @@ +-This is mpfr.info, produced by makeinfo version 5.2 from mpfr.texi. ++This is mpfr.info, produced by makeinfo version 6.0 from mpfr.texi. + + This manual documents how to install and use the Multiple Precision + Floating-Point Reliable Library, version 3.1.3. +@@ -55,7 +55,7 @@ + MPFR Copying Conditions + *********************** + +-The GNU MPFR library (or MPFR for short) is "free"; this means that ++The GNU MPFR library (or MPFR for short) is “free”; this means that + everyone is free to use it and free to redistribute it on a free basis. + The library is not in the public domain; it is copyrighted and there are + restrictions on its distribution, but these restrictions are designed to +@@ -418,7 +418,7 @@ + 4.2 Nomenclature and Types + ========================== + +-A "floating-point number", or "float" for short, is an arbitrary ++A “floating-point number”, or “float” for short, is an arbitrary + precision significand (also called mantissa) with a limited precision + exponent. The C data type for such objects is ‘mpfr_t’ (internally + defined as a one-element array of a structure, and ‘mpfr_ptr’ is the C +@@ -432,7 +432,7 @@ + to the other functions supported by MPFR. Unless documented otherwise, + the sign bit of a NaN is unspecified. + +-The "precision" is the number of bits used to represent the significand ++The “precision” is the number of bits used to represent the significand + of a floating-point number; the corresponding C data type is + ‘mpfr_prec_t’. The precision can be any integer between ‘MPFR_PREC_MIN’ + and ‘MPFR_PREC_MAX’. In the current implementation, ‘MPFR_PREC_MIN’ is +@@ -446,7 +446,7 @@ + may abort, crash or have undefined behavior (depending on your C + implementation). + +-The "rounding mode" specifies the way to round the result of a ++The “rounding mode” specifies the way to round the result of a + floating-point operation, in case the exact result can not be + represented exactly in the destination significand; the corresponding C + data type is ‘mpfr_rnd_t’. +@@ -499,14 +499,14 @@ + representable numbers, it is rounded to the one with the least + significant bit set to zero. For example, the number 2.5, which is + represented by (10.1) in binary, is rounded to (10.0)=2 with a precision +-of two bits, and not to (11.0)=3. This rule avoids the "drift" ++of two bits, and not to (11.0)=3. This rule avoids the “drift” + phenomenon mentioned by Knuth in volume 2 of The Art of Computer + Programming (Section 4.2.2). + + Most MPFR functions take as first argument the destination variable, + as second and following arguments the input variables, as last argument + a rounding mode, and have a return value of type ‘int’, called the +-"ternary value". The value stored in the destination variable is ++“ternary value”. The value stored in the destination variable is + correctly rounded, i.e., MPFR behaves as if it computed the result with + an infinite precision, then rounded it to the precision of this + variable. The input variables are regarded as exact (in particular, +@@ -572,15 +572,18 @@ + When the input point is in the closure of the domain of the + mathematical function and an input argument is +0 (resp. −0), one + considers the limit when the corresponding argument approaches 0 from +-above (resp. below). If the limit is not defined (e.g., ‘mpfr_log’ on +-−0), the behavior is specified in the description of the MPFR function. ++above (resp. below), if possible. If the limit is not defined (e.g., ++‘mpfr_sqrt’ and ‘mpfr_log’ on −0), the behavior is specified in the ++description of the MPFR function, but must be consistent with the rule ++from the above paragraph (e.g., ‘mpfr_log’ on ±0 gives −Inf). + + When the result is equal to 0, its sign is determined by considering + the limit as if the input point were not in the domain: If one + approaches 0 from above (resp. below), the result is +0 (resp. −0); for +-example, ‘mpfr_sin’ on +0 gives +0. In the other cases, the sign is +-specified in the description of the MPFR function; for example +-‘mpfr_max’ on −0 and +0 gives +0. ++example, ‘mpfr_sin’ on −0 gives −0 and ‘mpfr_acos’ on 1 gives +0 (in all ++rounding modes). In the other cases, the sign is specified in the ++description of the MPFR function; for example ‘mpfr_max’ on −0 and +0 ++gives +0. + + When the input point is not in the closure of the domain of the + function, the result is NaN. Example: ‘mpfr_sqrt’ on −17 gives NaN. +@@ -590,8 +593,8 @@ + numbers; such a case is always explicitly specified in *note MPFR + Interface::. Example: ‘mpfr_hypot’ on (NaN,0) gives NaN, but + ‘mpfr_hypot’ on (NaN,+Inf) gives +Inf (as specified in *note Special +-Functions::), since for any finite input X, ‘mpfr_hypot’ on (X,+Inf) +-gives +Inf. ++Functions::), since for any finite or infinite input X, ‘mpfr_hypot’ on ++(X,+Inf) gives +Inf. + +  + File: mpfr.info, Node: Exceptions, Next: Memory Handling, Prev: Floating-Point Values on Special Numbers, Up: MPFR Basics +@@ -1253,8 +1256,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_add_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 + OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) + 0 = ++ Set ROP to OP1 + OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) + 0 = + (+0) and (−0) + 0 = (−0)). The ‘mpfr_add_d’ function assumes that + the radix of the ‘double’ type is a power of 2, with a precision at + most that declared by the C implementation (macro +@@ -1280,8 +1284,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_sub_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 - OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) − 0 = ++ Set ROP to OP1 - OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) − 0 = + (+0), (−0) − 0 = (−0), 0 − (+0) = (−0) and 0 − (−0) = (+0)). The + same restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_sub’ and + ‘mpfr_sub_d’. +@@ -1300,7 +1305,7 @@ + mpfr_rnd_t RND) + Set ROP to OP1 times OP2 rounded in the direction RND. When a + result is zero, its sign is the product of the signs of the +- operands (for types having no signed zero, it is considered ++ operands (for types having no signed zeros, 0 is considered + positive). The same restrictions than for ‘mpfr_add_d’ apply to + ‘mpfr_mul_d’. + +@@ -1327,21 +1332,24 @@ + mpfr_rnd_t RND) + Set ROP to OP1/OP2 rounded in the direction RND. When a result is + zero, its sign is the product of the signs of the operands (for +- types having no signed zero, it is considered positive). The same ++ types having no signed zeros, 0 is considered positive). The same + restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_div’ and + ‘mpfr_div_d’. + + -- Function: int mpfr_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_sqrt_ui (mpfr_t ROP, unsigned long int OP, + mpfr_rnd_t RND) +- Set ROP to the square root of OP rounded in the direction RND (set +- ROP to −0 if OP is −0, to be consistent with the IEEE 754 +- standard). Set ROP to NaN if OP is negative. ++ Set ROP to the square root of OP rounded in the direction RND. Set ++ ROP to −0 if OP is −0, to be consistent with the IEEE 754 standard. ++ Set ROP to NaN if OP is negative. + + -- Function: int mpfr_rec_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the reciprocal square root of OP rounded in the + direction RND. Set ROP to +Inf if OP is ±0, +0 if OP is +Inf, and +- NaN if OP is negative. ++ NaN if OP is negative. Warning! Therefore the result on −0 is ++ different from the one of the rSqrt function recommended by the ++ IEEE 754-2008 standard (Section 9.2.1), which is −Inf instead of ++ +Inf. + + -- Function: int mpfr_cbrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_root (mpfr_t ROP, mpfr_t OP, unsigned long int K, +@@ -1515,8 +1523,10 @@ + -- Function: int mpfr_log2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_log10 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the natural logarithm of OP, log2(OP) or log10(OP), +- respectively, rounded in the direction RND. Set ROP to −Inf if OP +- is −0 (i.e., the sign of the zero has no influence on the result). ++ respectively, rounded in the direction RND. Set ROP to +0 if OP is ++ 1 (in all rounding modes), for consistency with the ISO C99 and ++ IEEE 754-2008 standards. Set ROP to −Inf if OP is ±0 (i.e., the ++ sign of the zero has no influence on the result). + + -- Function: int mpfr_exp (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_exp2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) +@@ -1649,17 +1659,21 @@ + + -- Function: int mpfr_lngamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the Gamma function on OP, +- rounded in the direction RND. When −2K−1 <= OP <= −2K, K being a +- non-negative integer, ROP is set to NaN. See also ‘mpfr_lgamma’. ++ rounded in the direction RND. When OP is 1 or 2, set ROP to +0 (in ++ all rounding modes). When OP is an infinity or a nonpositive ++ integer, set ROP to +Inf, following the general rules on special ++ values. When −2K−1 < OP < −2K, K being a nonnegative integer, set ++ ROP to NaN. See also ‘mpfr_lgamma’. + + -- Function: int mpfr_lgamma (mpfr_t ROP, int *SIGNP, mpfr_t OP, + mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the absolute value of the + Gamma function on OP, rounded in the direction RND. The sign (1 or + −1) of Gamma(OP) is returned in the object pointed to by SIGNP. +- When OP is an infinity or a non-positive integer, set ROP to +Inf. +- When OP is NaN, −Inf or a negative integer, *SIGNP is undefined, +- and when OP is ±0, *SIGNP is the sign of the zero. ++ When OP is 1 or 2, set ROP to +0 (in all rounding modes). When OP ++ is an infinity or a nonpositive integer, set ROP to +Inf. When OP ++ is NaN, −Inf or a negative integer, *SIGNP is undefined, and when ++ OP is ±0, *SIGNP is the sign of the zero. + + -- Function: int mpfr_digamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the Digamma (sometimes also called Psi) +@@ -1703,7 +1717,10 @@ + -- Function: int mpfr_fms (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, mpfr_t + OP3, mpfr_rnd_t RND) + Set ROP to (OP1 times OP2) + OP3 (resp. (OP1 times OP2) - OP3) +- rounded in the direction RND. ++ rounded in the direction RND. Concerning special values (signed ++ zeros, infinities, NaN), these functions behave like a ++ multiplication followed by a separate addition or subtraction. ++ That is, the fused operation matters only for rounding. + + -- Function: int mpfr_agm (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, + mpfr_rnd_t RND) +@@ -1717,9 +1734,10 @@ + RND) + Set ROP to the Euclidean norm of X and Y, i.e., the square root of + the sum of the squares of X and Y, rounded in the direction RND. +- Special values are handled as described in Section F.9.4.3 of the +- ISO C99 and IEEE 754-2008 standards: If X or Y is an infinity, then +- +Inf is returned in ROP, even if the other number is NaN. ++ Special values are handled as described in the ISO C99 (Section ++ F.9.4.3) and IEEE 754-2008 (Section 9.2.1) standards: If X or Y is ++ an infinity, then +Inf is returned in ROP, even if the other number ++ is NaN. + + -- Function: int mpfr_ai (mpfr_t ROP, mpfr_t X, mpfr_rnd_t RND) + Set ROP to the value of the Airy function Ai on X, rounded in the +@@ -2670,7 +2688,7 @@ + 5.16 Internals + ============== + +-A "limb" means the part of a multi-precision number that fits in a ++A “limb” means the part of a multi-precision number that fits in a + single word. Usually a limb contains 32 or 64 bits. The C data type + for a limb is ‘mp_limb_t’. + +@@ -3140,7 +3158,7 @@ + 0. PREAMBLE + + The purpose of this License is to make a manual, textbook, or other +- functional and useful document "free" in the sense of freedom: to ++ functional and useful document “free” in the sense of freedom: to + assure everyone the effective freedom to copy and redistribute it, + with or without modifying it, either commercially or + noncommercially. Secondarily, this License preserves for the +@@ -3655,9 +3673,9 @@ + * Menu: + + * mpfr_abs: Basic Arithmetic Functions. +- (line 160) +-* mpfr_acos: Special Functions. (line 51) +-* mpfr_acosh: Special Functions. (line 115) ++ (line 165) ++* mpfr_acos: Special Functions. (line 53) ++* mpfr_acosh: Special Functions. (line 117) + * mpfr_add: Basic Arithmetic Functions. + (line 6) + * mpfr_add_d: Basic Arithmetic Functions. +@@ -3670,15 +3688,15 @@ + (line 8) + * mpfr_add_z: Basic Arithmetic Functions. + (line 14) +-* mpfr_agm: Special Functions. (line 210) +-* mpfr_ai: Special Functions. (line 226) +-* mpfr_asin: Special Functions. (line 52) +-* mpfr_asinh: Special Functions. (line 116) ++* mpfr_agm: Special Functions. (line 219) ++* mpfr_ai: Special Functions. (line 236) ++* mpfr_asin: Special Functions. (line 54) ++* mpfr_asinh: Special Functions. (line 118) + * mpfr_asprintf: Formatted Output Functions. + (line 193) +-* mpfr_atan: Special Functions. (line 53) +-* mpfr_atan2: Special Functions. (line 63) +-* mpfr_atanh: Special Functions. (line 117) ++* mpfr_atan: Special Functions. (line 55) ++* mpfr_atan2: Special Functions. (line 65) ++* mpfr_atanh: Special Functions. (line 119) + * mpfr_buildopt_decimal_p: Miscellaneous Functions. + (line 162) + * mpfr_buildopt_gmpinternals_p: Miscellaneous Functions. +@@ -3690,7 +3708,7 @@ + * mpfr_can_round: Rounding Related Functions. + (line 39) + * mpfr_cbrt: Basic Arithmetic Functions. +- (line 108) ++ (line 113) + * mpfr_ceil: Integer Related Functions. + (line 7) + * mpfr_check_range: Exception Related Functions. +@@ -3735,18 +3753,18 @@ + (line 27) + * mpfr_cmp_z: Comparison Functions. + (line 11) +-* mpfr_const_catalan: Special Functions. (line 237) +-* mpfr_const_euler: Special Functions. (line 236) +-* mpfr_const_log2: Special Functions. (line 234) +-* mpfr_const_pi: Special Functions. (line 235) ++* mpfr_const_catalan: Special Functions. (line 247) ++* mpfr_const_euler: Special Functions. (line 246) ++* mpfr_const_log2: Special Functions. (line 244) ++* mpfr_const_pi: Special Functions. (line 245) + * mpfr_copysign: Miscellaneous Functions. + (line 109) +-* mpfr_cos: Special Functions. (line 29) +-* mpfr_cosh: Special Functions. (line 95) +-* mpfr_cot: Special Functions. (line 47) +-* mpfr_coth: Special Functions. (line 111) +-* mpfr_csc: Special Functions. (line 46) +-* mpfr_csch: Special Functions. (line 110) ++* mpfr_cos: Special Functions. (line 31) ++* mpfr_cosh: Special Functions. (line 97) ++* mpfr_cot: Special Functions. (line 49) ++* mpfr_coth: Special Functions. (line 113) ++* mpfr_csc: Special Functions. (line 48) ++* mpfr_csch: Special Functions. (line 112) + * mpfr_custom_get_exp: Custom Interface. (line 75) + * mpfr_custom_get_kind: Custom Interface. (line 65) + * mpfr_custom_get_significand: Custom Interface. (line 70) +@@ -3756,47 +3774,47 @@ + * mpfr_custom_move: Custom Interface. (line 82) + * MPFR_DECL_INIT: Initialization Functions. + (line 74) +-* mpfr_digamma: Special Functions. (line 166) ++* mpfr_digamma: Special Functions. (line 172) + * mpfr_dim: Basic Arithmetic Functions. +- (line 166) ++ (line 171) + * mpfr_div: Basic Arithmetic Functions. +- (line 72) ++ (line 74) + * mpfr_divby0_p: Exception Related Functions. + (line 134) + * mpfr_div_2exp: Compatibility with MPF. + (line 49) + * mpfr_div_2si: Basic Arithmetic Functions. +- (line 181) ++ (line 186) + * mpfr_div_2ui: Basic Arithmetic Functions. +- (line 179) ++ (line 184) + * mpfr_div_d: Basic Arithmetic Functions. +- (line 84) ++ (line 86) + * mpfr_div_q: Basic Arithmetic Functions. +- (line 88) ++ (line 90) + * mpfr_div_si: Basic Arithmetic Functions. +- (line 80) ++ (line 82) + * mpfr_div_ui: Basic Arithmetic Functions. +- (line 76) ++ (line 78) + * mpfr_div_z: Basic Arithmetic Functions. +- (line 86) ++ (line 88) + * mpfr_d_div: Basic Arithmetic Functions. +- (line 82) ++ (line 84) + * mpfr_d_sub: Basic Arithmetic Functions. +- (line 35) +-* mpfr_eint: Special Functions. (line 133) ++ (line 36) ++* mpfr_eint: Special Functions. (line 135) + * mpfr_eq: Compatibility with MPF. + (line 28) + * mpfr_equal_p: Comparison Functions. + (line 59) + * mpfr_erangeflag_p: Exception Related Functions. + (line 137) +-* mpfr_erf: Special Functions. (line 177) +-* mpfr_erfc: Special Functions. (line 178) +-* mpfr_exp: Special Functions. (line 23) +-* mpfr_exp10: Special Functions. (line 25) +-* mpfr_exp2: Special Functions. (line 24) +-* mpfr_expm1: Special Functions. (line 129) +-* mpfr_fac_ui: Special Functions. (line 121) ++* mpfr_erf: Special Functions. (line 183) ++* mpfr_erfc: Special Functions. (line 184) ++* mpfr_exp: Special Functions. (line 25) ++* mpfr_exp10: Special Functions. (line 27) ++* mpfr_exp2: Special Functions. (line 26) ++* mpfr_expm1: Special Functions. (line 131) ++* mpfr_fac_ui: Special Functions. (line 123) + * mpfr_fits_intmax_p: Conversion Functions. + (line 150) + * mpfr_fits_sint_p: Conversion Functions. +@@ -3815,20 +3833,20 @@ + (line 147) + * mpfr_floor: Integer Related Functions. + (line 8) +-* mpfr_fma: Special Functions. (line 203) ++* mpfr_fma: Special Functions. (line 209) + * mpfr_fmod: Integer Related Functions. + (line 92) +-* mpfr_fms: Special Functions. (line 205) ++* mpfr_fms: Special Functions. (line 211) + * mpfr_fprintf: Formatted Output Functions. + (line 157) + * mpfr_frac: Integer Related Functions. + (line 76) +-* mpfr_free_cache: Special Functions. (line 244) ++* mpfr_free_cache: Special Functions. (line 254) + * mpfr_free_str: Conversion Functions. + (line 137) + * mpfr_frexp: Conversion Functions. + (line 45) +-* mpfr_gamma: Special Functions. (line 148) ++* mpfr_gamma: Special Functions. (line 150) + * mpfr_get_d: Conversion Functions. + (line 7) + * mpfr_get_decimal64: Conversion Functions. +@@ -3887,7 +3905,7 @@ + (line 56) + * mpfr_greater_p: Comparison Functions. + (line 55) +-* mpfr_hypot: Special Functions. (line 218) ++* mpfr_hypot: Special Functions. (line 227) + * mpfr_inexflag_p: Exception Related Functions. + (line 136) + * mpfr_inf_p: Comparison Functions. +@@ -3922,21 +3940,21 @@ + (line 31) + * mpfr_integer_p: Integer Related Functions. + (line 119) +-* mpfr_j0: Special Functions. (line 182) +-* mpfr_j1: Special Functions. (line 183) +-* mpfr_jn: Special Functions. (line 184) ++* mpfr_j0: Special Functions. (line 188) ++* mpfr_j1: Special Functions. (line 189) ++* mpfr_jn: Special Functions. (line 190) + * mpfr_lessequal_p: Comparison Functions. + (line 58) + * mpfr_lessgreater_p: Comparison Functions. + (line 64) + * mpfr_less_p: Comparison Functions. + (line 57) +-* mpfr_lgamma: Special Functions. (line 157) +-* mpfr_li2: Special Functions. (line 143) +-* mpfr_lngamma: Special Functions. (line 152) ++* mpfr_lgamma: Special Functions. (line 162) ++* mpfr_li2: Special Functions. (line 145) ++* mpfr_lngamma: Special Functions. (line 154) + * mpfr_log: Special Functions. (line 16) + * mpfr_log10: Special Functions. (line 18) +-* mpfr_log1p: Special Functions. (line 125) ++* mpfr_log1p: Special Functions. (line 127) + * mpfr_log2: Special Functions. (line 17) + * mpfr_max: Miscellaneous Functions. + (line 22) +@@ -3947,29 +3965,29 @@ + * mpfr_modf: Integer Related Functions. + (line 82) + * mpfr_mul: Basic Arithmetic Functions. +- (line 51) ++ (line 53) + * mpfr_mul_2exp: Compatibility with MPF. + (line 47) + * mpfr_mul_2si: Basic Arithmetic Functions. +- (line 174) ++ (line 179) + * mpfr_mul_2ui: Basic Arithmetic Functions. +- (line 172) ++ (line 177) + * mpfr_mul_d: Basic Arithmetic Functions. +- (line 57) ++ (line 59) + * mpfr_mul_q: Basic Arithmetic Functions. +- (line 61) ++ (line 63) + * mpfr_mul_si: Basic Arithmetic Functions. +- (line 55) ++ (line 57) + * mpfr_mul_ui: Basic Arithmetic Functions. +- (line 53) ++ (line 55) + * mpfr_mul_z: Basic Arithmetic Functions. +- (line 59) ++ (line 61) + * mpfr_nanflag_p: Exception Related Functions. + (line 135) + * mpfr_nan_p: Comparison Functions. + (line 39) + * mpfr_neg: Basic Arithmetic Functions. +- (line 159) ++ (line 164) + * mpfr_nextabove: Miscellaneous Functions. + (line 15) + * mpfr_nextbelow: Miscellaneous Functions. +@@ -3983,13 +4001,13 @@ + * mpfr_overflow_p: Exception Related Functions. + (line 133) + * mpfr_pow: Basic Arithmetic Functions. +- (line 116) ++ (line 121) + * mpfr_pow_si: Basic Arithmetic Functions. +- (line 120) ++ (line 125) + * mpfr_pow_ui: Basic Arithmetic Functions. +- (line 118) ++ (line 123) + * mpfr_pow_z: Basic Arithmetic Functions. +- (line 122) ++ (line 127) + * mpfr_prec_round: Rounding Related Functions. + (line 13) + * ‘mpfr_prec_t’: Nomenclature and Types. +@@ -3999,7 +4017,7 @@ + * mpfr_print_rnd_mode: Rounding Related Functions. + (line 71) + * mpfr_rec_sqrt: Basic Arithmetic Functions. +- (line 103) ++ (line 105) + * mpfr_regular_p: Comparison Functions. + (line 43) + * mpfr_reldiff: Compatibility with MPF. +@@ -4021,11 +4039,11 @@ + * ‘mpfr_rnd_t’: Nomenclature and Types. + (line 34) + * mpfr_root: Basic Arithmetic Functions. +- (line 109) ++ (line 114) + * mpfr_round: Integer Related Functions. + (line 9) +-* mpfr_sec: Special Functions. (line 45) +-* mpfr_sech: Special Functions. (line 109) ++* mpfr_sec: Special Functions. (line 47) ++* mpfr_sech: Special Functions. (line 111) + * mpfr_set: Assignment Functions. + (line 9) + * mpfr_setsign: Miscellaneous Functions. +@@ -4100,57 +4118,57 @@ + (line 49) + * mpfr_signbit: Miscellaneous Functions. + (line 99) +-* mpfr_sin: Special Functions. (line 30) +-* mpfr_sinh: Special Functions. (line 96) +-* mpfr_sinh_cosh: Special Functions. (line 101) +-* mpfr_sin_cos: Special Functions. (line 35) ++* mpfr_sin: Special Functions. (line 32) ++* mpfr_sinh: Special Functions. (line 98) ++* mpfr_sinh_cosh: Special Functions. (line 103) ++* mpfr_sin_cos: Special Functions. (line 37) + * mpfr_si_div: Basic Arithmetic Functions. +- (line 78) ++ (line 80) + * mpfr_si_sub: Basic Arithmetic Functions. +- (line 31) ++ (line 32) + * mpfr_snprintf: Formatted Output Functions. + (line 180) + * mpfr_sprintf: Formatted Output Functions. + (line 170) + * mpfr_sqr: Basic Arithmetic Functions. +- (line 69) ++ (line 71) + * mpfr_sqrt: Basic Arithmetic Functions. +- (line 96) ++ (line 98) + * mpfr_sqrt_ui: Basic Arithmetic Functions. +- (line 97) ++ (line 99) + * mpfr_strtofr: Assignment Functions. + (line 80) + * mpfr_sub: Basic Arithmetic Functions. +- (line 25) ++ (line 26) + * mpfr_subnormalize: Exception Related Functions. + (line 60) + * mpfr_sub_d: Basic Arithmetic Functions. +- (line 37) ++ (line 38) + * mpfr_sub_q: Basic Arithmetic Functions. +- (line 43) ++ (line 44) + * mpfr_sub_si: Basic Arithmetic Functions. +- (line 33) ++ (line 34) + * mpfr_sub_ui: Basic Arithmetic Functions. +- (line 29) ++ (line 30) + * mpfr_sub_z: Basic Arithmetic Functions. +- (line 41) +-* mpfr_sum: Special Functions. (line 252) ++ (line 42) ++* mpfr_sum: Special Functions. (line 262) + * mpfr_swap: Assignment Functions. + (line 150) + * ‘mpfr_t’: Nomenclature and Types. + (line 6) +-* mpfr_tan: Special Functions. (line 31) +-* mpfr_tanh: Special Functions. (line 97) ++* mpfr_tan: Special Functions. (line 33) ++* mpfr_tanh: Special Functions. (line 99) + * mpfr_trunc: Integer Related Functions. + (line 10) + * mpfr_ui_div: Basic Arithmetic Functions. +- (line 74) ++ (line 76) + * mpfr_ui_pow: Basic Arithmetic Functions. +- (line 126) ++ (line 131) + * mpfr_ui_pow_ui: Basic Arithmetic Functions. +- (line 124) ++ (line 129) + * mpfr_ui_sub: Basic Arithmetic Functions. +- (line 27) ++ (line 28) + * mpfr_underflow_p: Exception Related Functions. + (line 132) + * mpfr_unordered_p: Comparison Functions. +@@ -4181,61 +4199,61 @@ + (line 182) + * mpfr_vsprintf: Formatted Output Functions. + (line 171) +-* mpfr_y0: Special Functions. (line 193) +-* mpfr_y1: Special Functions. (line 194) +-* mpfr_yn: Special Functions. (line 195) ++* mpfr_y0: Special Functions. (line 199) ++* mpfr_y1: Special Functions. (line 200) ++* mpfr_yn: Special Functions. (line 201) + * mpfr_zero_p: Comparison Functions. + (line 42) +-* mpfr_zeta: Special Functions. (line 171) +-* mpfr_zeta_ui: Special Functions. (line 172) ++* mpfr_zeta: Special Functions. (line 177) ++* mpfr_zeta_ui: Special Functions. (line 178) + * mpfr_z_sub: Basic Arithmetic Functions. +- (line 39) ++ (line 40) + + +  + Tag Table: + Node: Top775 + Node: Copying2007 +-Node: Introduction to MPFR3766 +-Node: Installing MPFR5880 +-Node: Reporting Bugs11323 +-Node: MPFR Basics13353 +-Node: Headers and Libraries13669 +-Node: Nomenclature and Types16828 +-Node: MPFR Variable Conventions18874 +-Node: Rounding Modes20418 +-Ref: ternary value21544 +-Node: Floating-Point Values on Special Numbers23526 +-Node: Exceptions26572 +-Node: Memory Handling29749 +-Node: MPFR Interface30894 +-Node: Initialization Functions33008 +-Node: Assignment Functions40318 +-Node: Combined Initialization and Assignment Functions49673 +-Node: Conversion Functions50974 +-Node: Basic Arithmetic Functions60035 +-Node: Comparison Functions69200 +-Node: Special Functions72687 +-Node: Input and Output Functions86672 +-Node: Formatted Output Functions88644 +-Node: Integer Related Functions98431 +-Node: Rounding Related Functions105051 +-Node: Miscellaneous Functions108888 +-Node: Exception Related Functions117568 +-Node: Compatibility with MPF124386 +-Node: Custom Interface127127 +-Node: Internals131526 +-Node: API Compatibility133066 +-Node: Type and Macro Changes134995 +-Node: Added Functions137844 +-Node: Changed Functions141132 +-Node: Removed Functions145545 +-Node: Other Changes145973 +-Node: Contributors147576 +-Node: References150219 +-Node: GNU Free Documentation License151973 +-Node: Concept Index174562 +-Node: Function and Type Index180659 ++Node: Introduction to MPFR3770 ++Node: Installing MPFR5884 ++Node: Reporting Bugs11327 ++Node: MPFR Basics13357 ++Node: Headers and Libraries13673 ++Node: Nomenclature and Types16832 ++Node: MPFR Variable Conventions18894 ++Node: Rounding Modes20438 ++Ref: ternary value21568 ++Node: Floating-Point Values on Special Numbers23554 ++Node: Exceptions26813 ++Node: Memory Handling29990 ++Node: MPFR Interface31135 ++Node: Initialization Functions33249 ++Node: Assignment Functions40559 ++Node: Combined Initialization and Assignment Functions49914 ++Node: Conversion Functions51215 ++Node: Basic Arithmetic Functions60276 ++Node: Comparison Functions69777 ++Node: Special Functions73264 ++Node: Input and Output Functions87862 ++Node: Formatted Output Functions89834 ++Node: Integer Related Functions99621 ++Node: Rounding Related Functions106241 ++Node: Miscellaneous Functions110078 ++Node: Exception Related Functions118758 ++Node: Compatibility with MPF125576 ++Node: Custom Interface128317 ++Node: Internals132716 ++Node: API Compatibility134260 ++Node: Type and Macro Changes136189 ++Node: Added Functions139038 ++Node: Changed Functions142326 ++Node: Removed Functions146739 ++Node: Other Changes147167 ++Node: Contributors148770 ++Node: References151413 ++Node: GNU Free Documentation License153167 ++Node: Concept Index175760 ++Node: Function and Type Index181857 +  + End Tag Table + +diff -Naurd mpfr-3.1.3-a/src/lngamma.c mpfr-3.1.3-b/src/lngamma.c +--- mpfr-3.1.3-a/src/lngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/lngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -603,16 +603,17 @@ + mpfr_get_prec (y), mpfr_log_prec, y, inex)); + + /* special cases */ +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x) || ++ (MPFR_IS_NEG (x) && mpfr_integer_p (x)))) + { +- if (MPFR_IS_NAN (x) || MPFR_IS_NEG (x)) ++ if (MPFR_IS_NAN (x)) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; + } +- else /* lngamma(+Inf) = lngamma(+0) = +Inf */ ++ else /* lngamma(+/-Inf) = lngamma(nonpositive integer) = +Inf */ + { +- if (MPFR_IS_ZERO (x)) ++ if (!MPFR_IS_INF (x)) + mpfr_set_divby0 (); + MPFR_SET_INF (y); + MPFR_SET_POS (y); +@@ -620,8 +621,8 @@ + } + } + +- /* if x < 0 and -2k-1 <= x <= -2k, then lngamma(x) = NaN */ +- if (MPFR_IS_NEG (x) && (unit_bit (x) == 0 || mpfr_integer_p (x))) ++ /* if -2k-1 < x < -2k <= 0, then lngamma(x) = NaN */ ++ if (MPFR_IS_NEG (x) && unit_bit (x) == 0) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3" ++#define MPFR_VERSION_STRING "3.1.3-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:49:24.042113845 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3"; ++ return "3.1.3-p1"; + } +diff -Naurd mpfr-3.1.3-a/tests/tlngamma.c mpfr-3.1.3-b/tests/tlngamma.c +--- mpfr-3.1.3-a/tests/tlngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tlngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -33,7 +33,7 @@ + special (void) + { + mpfr_t x, y; +- int inex; ++ int i, inex; + + mpfr_init (x); + mpfr_init (y); +@@ -46,25 +46,29 @@ + exit (1); + } + +- mpfr_set_inf (x, -1); ++ mpfr_set_inf (x, 1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(-Inf)\n"); ++ printf ("Error for lngamma(+Inf)\n"); + exit (1); + } + +- mpfr_set_inf (x, 1); ++ mpfr_set_inf (x, -1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(+Inf)\n"); ++ printf ("Error for lngamma(-Inf)\n"); + exit (1); + } + + mpfr_set_ui (x, 0, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(+0)\n"); + exit (1); +@@ -72,32 +76,58 @@ + + mpfr_set_ui (x, 0, MPFR_RNDN); + mpfr_neg (x, x, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(-0)\n"); + exit (1); + } + + mpfr_set_ui (x, 1, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(1)\n"); + exit (1); + } + +- mpfr_set_si (x, -1, MPFR_RNDN); +- mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ for (i = 1; i <= 5; i++) + { +- printf ("Error for lngamma(-1)\n"); +- exit (1); ++ int c; ++ ++ mpfr_set_si (x, -i, MPFR_RNDN); ++ mpfr_clear_flags (); ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) ++ { ++ printf ("Error for lngamma(-%d)\n", i); ++ exit (1); ++ } ++ if (i & 1) ++ { ++ mpfr_nextabove (x); ++ c = '+'; ++ } ++ else ++ { ++ mpfr_nextbelow (x); ++ c = '-'; ++ } ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_nan_p (y)) ++ { ++ printf ("Error for lngamma(-%d%cepsilon)\n", i, c); ++ exit (1); ++ } + } + + mpfr_set_ui (x, 2, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(2)\n"); + exit (1); +@@ -127,7 +157,7 @@ + mpfr_set_str (x, CHECK_X2, 10, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str (x, CHECK_Y2, 10, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp (y, x)) ++ if (mpfr_cmp0 (y, x)) + { + printf ("mpfr_lngamma("CHECK_X2") is wrong:\n" + "expected "); +@@ -143,7 +173,7 @@ + mpfr_lngamma (y, x, MPFR_RNDU); + mpfr_set_prec (x, 175); + mpfr_set_str_binary (x, "0.1010001100011101101011001101110010100001000001000001110011000001101100001111001001000101011011100100010101011110100111110101010100010011010010000101010111001100011000101111E7"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (1)\n"); + exit (1); +@@ -155,7 +185,7 @@ + mpfr_lngamma (x, y, MPFR_RNDZ); + mpfr_set_prec (y, 21); + mpfr_set_str_binary (y, "0.111000101000001100101E9"); +- if (MPFR_IS_NAN (x) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (120)\n"); + printf ("Expected "); mpfr_print_binary (y); puts (""); +@@ -169,7 +199,7 @@ + inex = mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 206); + mpfr_set_str_binary (x, "0.10000111011000000011100010101001100110001110000111100011000100100110110010001011011110101001111011110110000001010100111011010000000011100110110101100111000111010011110010000100010111101010001101000110101001E13"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (768)\n"); + exit (1); +@@ -185,7 +215,7 @@ + mpfr_set_str_binary (x, "0.1100E-66"); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str_binary (x, "0.1100E6"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(0.1100E-66)\n"); + exit (1); +@@ -199,7 +229,7 @@ + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 32); + mpfr_set_str_binary (x, "-0.10001000111011111011000010100010E207"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(-2^199+0.5)\n"); + printf ("Got "); +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:50:08.046573308 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:50:08.126574142 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-overflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:50:08.126574142 +0000 +@@ -1 +1 @@ +-3.1.3-p1 ++3.1.3-p2 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -49,7 +49,7 @@ + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +- else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || ++ else if (MPFR_UNLIKELY(n <= 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || + exp > __gmpfr_emax + n)) ) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 +@@ -32,7 +32,7 @@ + rnd_mode), + ("y[%Pu]=%.*Rg inexact=%d", mpfr_get_prec(y), mpfr_log_prec, y, inexact)); + +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (n == 0 || MPFR_IS_SINGULAR (x))) + return mpfr_set (y, x, rnd_mode); + else + { +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p1" ++#define MPFR_VERSION_STRING "3.1.3-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -39,7 +39,7 @@ + { + mpfr_exp_t exp = MPFR_GET_EXP (x); + MPFR_SETRAW (inexact, y, x, exp, rnd_mode); +- if (MPFR_UNLIKELY( n > 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || ++ if (MPFR_UNLIKELY(n >= 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || + exp > __gmpfr_emax - n))) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emin > MPFR_EMAX_MAX + n || +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:50:08.126574142 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p1"; ++ return "3.1.3-p2"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 +@@ -242,6 +242,76 @@ + large (MPFR_EMAX_MAX); + } + ++/* Cases where the function overflows on n = 0 when rounding is like ++ away from zero. */ ++static void ++overflow0 (mpfr_exp_t emax) ++{ ++ mpfr_exp_t old_emax; ++ mpfr_t x, y1, y2; ++ int neg, r, op; ++ static char *sop[4] = { "mul_2ui", "mul_2si", "div_2ui", "div_2si" }; ++ ++ old_emax = mpfr_get_emax (); ++ set_emax (emax); ++ ++ mpfr_init2 (x, 8); ++ mpfr_inits2 (6, y1, y2, (mpfr_ptr) 0); ++ ++ mpfr_set_inf (x, 1); ++ mpfr_nextbelow (x); ++ ++ for (neg = 0; neg <= 1; neg++) ++ { ++ RND_LOOP (r) ++ { ++ int inex1, inex2; ++ unsigned int flags1, flags2; ++ ++ /* Even if there isn't an overflow (rounding ~ toward zero), ++ the result is the same as the one of an overflow. */ ++ inex1 = mpfr_overflow (y1, (mpfr_rnd_t) r, neg ? -1 : 1); ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (mpfr_inf_p (y1)) ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ for (op = 0; op < 4; op++) ++ { ++ mpfr_clear_flags (); ++ inex2 = ++ op == 0 ? mpfr_mul_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 1 ? mpfr_mul_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 2 ? mpfr_div_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 3 ? mpfr_div_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ (MPFR_ASSERTN (0), 0); ++ flags2 = __gmpfr_flags; ++ if (!(mpfr_equal_p (y1, y2) && ++ SAME_SIGN (inex1, inex2) && ++ flags1 == flags2)) ++ { ++ printf ("Error in overflow0 for %s, mpfr_%s, emax = %" ++ MPFR_EXP_FSPEC "d,\nx = ", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r), sop[op], ++ (mpfr_eexp_t) emax); ++ mpfr_dump (x); ++ printf ("Expected "); ++ mpfr_dump (y1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (y2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } ++ mpfr_neg (x, x, MPFR_RNDN); ++ } ++ ++ mpfr_clears (x, y1, y2, (mpfr_ptr) 0); ++ set_emax (old_emax); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -334,6 +404,11 @@ + underflow0 (); + large0 (); + ++ if (mpfr_get_emax () != MPFR_EMAX_MAX) ++ overflow0 (mpfr_get_emax ()); ++ overflow0 (MPFR_EMAX_MAX); ++ overflow0 (-1); ++ + tests_end_mpfr (); + return 0; + } +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-17 08:54:48.592799981 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-17 08:54:48.616811495 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-underflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-17 08:54:48.616811495 +0000 +@@ -1 +1 @@ +-3.1.3-p2 ++3.1.3-p3 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -45,7 +45,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX - (n - 1) || + exp < __gmpfr_emin + (n - 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-17 08:54:48.608807656 +0000 +@@ -44,7 +44,9 @@ + if (MPFR_UNLIKELY (n >= diffexp)) /* exp - n <= emin - 1 */ + { + if (rnd_mode == MPFR_RNDN && +- (n > diffexp || (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ (n > diffexp || ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN (y)); + } +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-17 08:54:48.616811495 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p2" ++#define MPFR_VERSION_STRING "3.1.3-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -48,7 +48,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX + (n + 1) || + exp < __gmpfr_emin - (n + 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-17 08:54:48.616811495 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p2"; ++ return "3.1.3-p3"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-17 08:54:48.608807656 +0000 +@@ -50,77 +50,82 @@ + { + mpfr_t x, y, z1, z2; + mpfr_exp_t emin; +- int i, k; ++ int i, k, s; + int prec; + int rnd; + int div; + int inex1, inex2; + unsigned int flags1, flags2; + +- /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) +- * with emin = e, x = 1 + i/16, i in { -1, 0, 1 }, and k = 1 to 4, +- * by comparing the result with the one of a simple division. ++ /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) with ++ * emin = e, x = s * (1 + i/16), i in { -1, 0, 1 }, s in { -1, 1 }, and ++ * k = 1 to 4, by comparing the result with the one of a simple division. + */ + emin = mpfr_get_emin (); + set_emin (e); + mpfr_inits2 (8, x, y, (mpfr_ptr) 0); + for (i = 15; i <= 17; i++) +- { +- inex1 = mpfr_set_ui_2exp (x, i, -4, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- for (prec = 6; prec >= 3; prec -= 3) +- { +- mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); +- RND_LOOP (rnd) +- for (k = 1; k <= 4; k++) +- { +- /* The following one is assumed to be correct. */ +- inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- mpfr_clear_flags (); +- /* Do not use mpfr_div_ui to avoid the optimization +- by mpfr_div_2si. */ +- inex1 = mpfr_div (z1, y, z1, (mpfr_rnd_t) rnd); +- flags1 = __gmpfr_flags; +- +- for (div = 0; div <= 2; div++) ++ for (s = 1; s >= -1; s -= 2) ++ { ++ inex1 = mpfr_set_si_2exp (x, s * i, -4, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ for (prec = 6; prec >= 3; prec -= 3) ++ { ++ mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); ++ RND_LOOP (rnd) ++ for (k = 1; k <= 4; k++) + { ++ /* The following one is assumed to be correct. */ ++ inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); + mpfr_clear_flags (); +- inex2 = div == 0 ? +- mpfr_mul_2si (z2, x, e - k, (mpfr_rnd_t) rnd) : div == 1 ? +- mpfr_div_2si (z2, x, k - e, (mpfr_rnd_t) rnd) : +- mpfr_div_2ui (z2, x, k - e, (mpfr_rnd_t) rnd); +- flags2 = __gmpfr_flags; +- if (flags1 == flags2 && SAME_SIGN (inex1, inex2) && +- mpfr_equal_p (z1, z2)) +- continue; +- printf ("Error in underflow("); +- if (e == MPFR_EMIN_MIN) +- printf ("MPFR_EMIN_MIN"); +- else if (e == emin) +- printf ("default emin"); +- else if (e >= LONG_MIN) +- printf ("%ld", (long) e); +- else +- printf ("= LONG_MIN) ++ printf ("%ld", (long) e); ++ else ++ printf ("d1 or (np[n-1]=d1 and np[n-2]>=d0) here, ++ since we truncate the divisor at each step, but since {np,n} < D ++ originally, the largest possible partial quotient is B-1. */ ++ if (MPFR_UNLIKELY(np[n-1] > d1 || (np[n-1] == d1 && np[n-2] >= d0))) + q2 = ~ (mp_limb_t) 0; + else + udiv_qr_3by2 (q2, q1, q0, np[n - 1], np[n - 2], np[n - 3], +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-17 08:58:21.118986898 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-10-29 13:47:46.763900609 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p4"; ++ return "3.1.3-p5"; + } +diff -Naurd mpfr-3.1.3-a/tests/tdiv.c mpfr-3.1.3-b/tests/tdiv.c +--- mpfr-3.1.3-a/tests/tdiv.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tdiv.c 2015-10-29 13:47:46.751900855 +0000 +@@ -1099,6 +1099,69 @@ + mpfr_set_emax (old_emax); + } + ++/* Bug in mpfr_divhigh_n_basecase when all limbs of q (except the most ++ significant one) are B-1 where B=2^GMP_NUMB_BITS. Since we truncate ++ the divisor at each step, it might happen at some point that ++ (np[n-1],np[n-2]) > (d1,d0), and not only the equality. ++ Reported by Ricky Farr ++ ++ To get a failure, a MPFR_DIVHIGH_TAB entry below the MPFR_DIV_THRESHOLD ++ limit must have a value 0. With most mparam.h files, this cannot occur. */ ++static void ++test_20151023 (void) ++{ ++ mpfr_prec_t p; ++ mpfr_t n, d, q, q0; ++ int inex, i; ++ ++ for (p = GMP_NUMB_BITS; p <= 2000; p++) ++ { ++ mpfr_init2 (n, 2*p); ++ mpfr_init2 (d, p); ++ mpfr_init2 (q, p); ++ mpfr_init2 (q0, GMP_NUMB_BITS); ++ ++ /* generate a random divisor of p bits */ ++ mpfr_urandomb (d, RANDS); ++ /* generate a random quotient of GMP_NUMB_BITS bits */ ++ mpfr_urandomb (q0, RANDS); ++ /* zero-pad the quotient to p bits */ ++ inex = mpfr_prec_round (q0, p, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ ++ for (i = 0; i < 3; i++) ++ { ++ /* i=0: try with the original quotient xxx000...000 ++ i=1: try with the original quotient minus one ulp ++ i=2: try with the original quotient plus one ulp */ ++ if (i == 1) ++ mpfr_nextbelow (q0); ++ else if (i == 2) ++ { ++ mpfr_nextabove (q0); ++ mpfr_nextabove (q0); ++ } ++ ++ inex = mpfr_mul (n, d, q0, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_nextabove (n); ++ mpfr_div (q, n, d, MPFR_RNDN); ++ MPFR_ASSERTN(mpfr_cmp (q, q0) == 0); ++ ++ inex = mpfr_mul (n, d, q0, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_nextbelow (n); ++ mpfr_div (q, n, d, MPFR_RNDN); ++ MPFR_ASSERTN(mpfr_cmp (q, q0) == 0); ++ } ++ ++ mpfr_clear (n); ++ mpfr_clear (d); ++ mpfr_clear (q); ++ mpfr_clear (q0); ++ } ++} ++ + #define TEST_FUNCTION test_div + #define TWO_ARGS + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) +@@ -1219,6 +1282,7 @@ + consistency (); + test_20070603 (); + test_20070628 (); ++ test_20151023 (); + test_generic (2, 800, 50); + test_extreme (); + diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..0a925c97ef --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..f4a9aac776 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 29bdfe711f830e92f3442131f7b11f95fe9020d2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 13:51:40 +1300 Subject: [PATCH 041/722] Patch needed for older versions of libspatialite --- .../l/libspatialite/libspatialite-configure.ac.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch new file mode 100644 index 0000000000..aacff1481f --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch @@ -0,0 +1,12 @@ +diff -urN libspatialite-4.1.1.orig/configure libspatialite-4.1.1/configure +--- libspatialite-4.1.1.orig/configure 2013-06-29 08:53:15.000000000 +0200 ++++ libspatialite-4.1.1/configure 2014-04-02 11:37:56.484423000 +0200 +@@ -263,7 +263,7 @@ + LIBS="$GEOS_LDFLAGS" + AC_SEARCH_LIBS(GEOSTopologyPreserveSimplify,geos_c,,AC_MSG_ERROR([could not find libgeos_c - you may need to specify the directory of a geos-config file using --with-geosconfig])) + LIBS="$LIBS_SAVE" +- LIBS=$LIBS$GEOS_LDFLAGS' -lgeos_c' ++ LIBS="$LIBS $GEOS_LDFLAGS -lgeos_c" + + #----------------------------------------------------------------------- + # --enable-geosadvanced -- GitLab From b49f76d9db0d68b541194ce6cc77a92667c6027a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 15:27:04 +1300 Subject: [PATCH 042/722] Deleted libspatialite-4.1.1 and associated files --- .../libspatialite-4.1.1-goolf-1.5.14.eb | 27 ------------------- .../libspatialite-configure.ac.patch | 12 --------- 2 files changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb delete mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb deleted file mode 100644 index 8132d40673..0000000000 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libspatialite' -version = '4.1.1' - -homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" -description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." - -toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'usempi': False, 'pic': True} - -download_suffix = '' -source_urls = ['http://www.gaia-gis.it/gaia-sins/'] -sources = [SOURCE_TAR_GZ] - -patches = ['libspatialite-configure.ac.patch'] - -dependencies = [('FreeXL','1.0.0g'),('GEOS','3.3.5'), ('SQLite', '3.8.4.3'), ('PROJ', '4.8.0')] -configopts = '--disable-geosadvanced' -builddependencies = [('CMake', '2.8.10.2')] - -sanity_check_paths = { - 'files': ["lib/libspatialite.la"], - 'dirs': ["lib","include"] - } - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch deleted file mode 100644 index aacff1481f..0000000000 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -urN libspatialite-4.1.1.orig/configure libspatialite-4.1.1/configure ---- libspatialite-4.1.1.orig/configure 2013-06-29 08:53:15.000000000 +0200 -+++ libspatialite-4.1.1/configure 2014-04-02 11:37:56.484423000 +0200 -@@ -263,7 +263,7 @@ - LIBS="$GEOS_LDFLAGS" - AC_SEARCH_LIBS(GEOSTopologyPreserveSimplify,geos_c,,AC_MSG_ERROR([could not find libgeos_c - you may need to specify the directory of a geos-config file using --with-geosconfig])) - LIBS="$LIBS_SAVE" -- LIBS=$LIBS$GEOS_LDFLAGS' -lgeos_c' -+ LIBS="$LIBS $GEOS_LDFLAGS -lgeos_c" - - #----------------------------------------------------------------------- - # --enable-geosadvanced -- GitLab From d67d88a99ac9860c6a57151d3c5ce24e73c20c7f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 15:37:10 +1300 Subject: [PATCH 043/722] Rename ORCA-3.0.0 EasyConfig to that which is expected given version string --- ...0_0-linux_x86-64.eb => ORCA-3_0_0-linux_x86-64_openmpi_165.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_0-linux_x86-64.eb => ORCA-3_0_0-linux_x86-64_openmpi_165.eb} (100%) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb similarity index 100% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb -- GitLab From d447397f4f05bb119f8f6068323e7a5ec3e83e68 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 15:44:45 +1300 Subject: [PATCH 044/722] Older version of libspatialite, reinstated --- .../libspatialite-4.1.1-goolf-1.5.14.eb | 27 +++++++++++++++++++ .../libspatialite-configure.ac.patch | 12 +++++++++ 2 files changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..8132d40673 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.1.1' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = '' +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +patches = ['libspatialite-configure.ac.patch'] + +dependencies = [('FreeXL','1.0.0g'),('GEOS','3.3.5'), ('SQLite', '3.8.4.3'), ('PROJ', '4.8.0')] +configopts = '--disable-geosadvanced' +builddependencies = [('CMake', '2.8.10.2')] + +sanity_check_paths = { + 'files': ["lib/libspatialite.la"], + 'dirs': ["lib","include"] + } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch new file mode 100644 index 0000000000..aacff1481f --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch @@ -0,0 +1,12 @@ +diff -urN libspatialite-4.1.1.orig/configure libspatialite-4.1.1/configure +--- libspatialite-4.1.1.orig/configure 2013-06-29 08:53:15.000000000 +0200 ++++ libspatialite-4.1.1/configure 2014-04-02 11:37:56.484423000 +0200 +@@ -263,7 +263,7 @@ + LIBS="$GEOS_LDFLAGS" + AC_SEARCH_LIBS(GEOSTopologyPreserveSimplify,geos_c,,AC_MSG_ERROR([could not find libgeos_c - you may need to specify the directory of a geos-config file using --with-geosconfig])) + LIBS="$LIBS_SAVE" +- LIBS=$LIBS$GEOS_LDFLAGS' -lgeos_c' ++ LIBS="$LIBS $GEOS_LDFLAGS -lgeos_c" + + #----------------------------------------------------------------------- + # --enable-geosadvanced -- GitLab From 21d05c9574074a7c3dd736dd87e3754f98036012 Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 19 Feb 2016 09:56:21 +0200 Subject: [PATCH 045/722] modify easyconfig Boost-1.59.0-intel-2015b.eb --- easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb index 7461992321..61f63ebb4e 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b.eb @@ -4,6 +4,7 @@ version = '1.59.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" +configopts = '--without-libraries=python' toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'pic': True, 'usempi': True} -- GitLab From b0d79ea7c64b6afd599aed88c22d3eef04509edb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Feb 2016 19:23:16 +0100 Subject: [PATCH 046/722] non-parallel build of flex 2.6.0 --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index f20e1d0126..0c9f4d80a4 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -13,4 +13,6 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] dependencies = [('Bison', '3.0.4')] +parallel = 1 + moduleclass = 'lang' -- GitLab From 78b5df7b4437faf94ba8ea6b484e097973e27154 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 22 Feb 2016 12:49:20 +1300 Subject: [PATCH 047/722] Removed older version of libspatialite --- .../libspatialite-4.1.1-goolf-1.5.14.eb | 27 ------------------- .../libspatialite-configure.ac.patch | 12 --------- 2 files changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb delete mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb deleted file mode 100644 index 8132d40673..0000000000 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.1.1-goolf-1.5.14.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libspatialite' -version = '4.1.1' - -homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" -description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." - -toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'usempi': False, 'pic': True} - -download_suffix = '' -source_urls = ['http://www.gaia-gis.it/gaia-sins/'] -sources = [SOURCE_TAR_GZ] - -patches = ['libspatialite-configure.ac.patch'] - -dependencies = [('FreeXL','1.0.0g'),('GEOS','3.3.5'), ('SQLite', '3.8.4.3'), ('PROJ', '4.8.0')] -configopts = '--disable-geosadvanced' -builddependencies = [('CMake', '2.8.10.2')] - -sanity_check_paths = { - 'files': ["lib/libspatialite.la"], - 'dirs': ["lib","include"] - } - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch b/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch deleted file mode 100644 index aacff1481f..0000000000 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-configure.ac.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -urN libspatialite-4.1.1.orig/configure libspatialite-4.1.1/configure ---- libspatialite-4.1.1.orig/configure 2013-06-29 08:53:15.000000000 +0200 -+++ libspatialite-4.1.1/configure 2014-04-02 11:37:56.484423000 +0200 -@@ -263,7 +263,7 @@ - LIBS="$GEOS_LDFLAGS" - AC_SEARCH_LIBS(GEOSTopologyPreserveSimplify,geos_c,,AC_MSG_ERROR([could not find libgeos_c - you may need to specify the directory of a geos-config file using --with-geosconfig])) - LIBS="$LIBS_SAVE" -- LIBS=$LIBS$GEOS_LDFLAGS' -lgeos_c' -+ LIBS="$LIBS $GEOS_LDFLAGS -lgeos_c" - - #----------------------------------------------------------------------- - # --enable-geosadvanced -- GitLab From 9f4b14efcfb9f49ad9a019c7221341b2cb879bd9 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 22 Feb 2016 12:52:30 +1300 Subject: [PATCH 048/722] Removed ec for libspatialite 4.3.0 with the Intel compiler suite --- .../libspatialite-4.3.0-intel-2015a.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb deleted file mode 100644 index 732c224f99..0000000000 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0-intel-2015a.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libspatialite' -version = '4.3.0' - -homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" -description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." - -toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'usempi': False, 'pic': True} - -download_suffix = '' -source_urls = ['http://www.gaia-gis.it/gaia-sins/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('FreeXL','1.0.1'), - ('GEOS','3.3.9'), - ('SQLite', '3.8.9'), - ('PROJ', '4.9.1'), -] - -configopts = '--disable-geosadvanced' - -builddependencies = [('CMake', '3.2.2')] - -sanity_check_paths = { - 'files': ["lib/libspatialite.la"], - 'dirs': ["lib","include"] - } - -moduleclass = 'lib' -- GitLab From bed52ee87acb7282f5e577ca7107cd77a4570a3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2016 12:05:26 +0100 Subject: [PATCH 049/722] fix minor style issues in libspatialite easyconfig --- .../libspatialite-4.3.0a-foss-2015a.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb index 0c50d9148b..9c107ea9d9 100644 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2015a.eb @@ -4,12 +4,12 @@ name = 'libspatialite' version = '4.3.0a' homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" -description = "SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities." +description = """SpatiaLite is an open source library intended to extend the SQLite core to support + fully fledged Spatial SQL capabilities.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'usempi': False, 'pic': True} -download_suffix = '' source_urls = ['http://www.gaia-gis.it/gaia-sins/'] sources = [SOURCE_TAR_GZ] @@ -20,13 +20,13 @@ dependencies = [ ('PROJ', '4.9.1'), ] -configopts = '--disable-geosadvanced' - builddependencies = [('CMake', '3.4.1')] +configopts = '--disable-geosadvanced' + sanity_check_paths = { - 'files': ["lib/libspatialite.la"], - 'dirs': ["lib","include"] - } + 'files': ['include/spatialite.h', 'lib/libspatialite.a', 'lib/libspatialite.%s' % SHLIB_EXT], + 'dirs': ['include/spatialite'], +} moduleclass = 'lib' -- GitLab From 992f0591971ca3c922def68b7ab40e1556b40853 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 24 Feb 2016 14:13:55 +1300 Subject: [PATCH 050/722] New EasyConfig for non-Python version of libxml2 2.9.3 with the foss 2015a toolchain --- .../l/libxml2/libxml2-2.9.3-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb new file mode 100644 index 0000000000..7c1a817fb6 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [ + ('zlib', '1.2.8'), +] + +moduleclass = 'lib' -- GitLab From 3021683dd3556e76a3a06e229d4e338153d82764 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 24 Feb 2016 14:22:59 +1300 Subject: [PATCH 051/722] No longer require python bindings for libxml2 dependency --- easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb index fdbd875ff2..001e2879da 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('netCDF', '4.3.3.1'), ('HDF5', '1.8.16'), ('expat', '2.1.0'), - ('libxml2', '2.9.3', '-Python-2.7.11'), + ('libxml2', '2.9.3'), ('zlib', '1.2.8'), ] -- GitLab From b0d06e61a6bb264589f31d972212e831480b7c76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2016 17:56:10 +0100 Subject: [PATCH 052/722] add binutils as dependency in flex easyconfig --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index 0c9f4d80a4..e1a9437774 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -13,6 +13,9 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] dependencies = [('Bison', '3.0.4')] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + parallel = 1 moduleclass = 'lang' -- GitLab From b28601235af520ecfd1a97b6375802e123717d2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2016 21:04:26 +0100 Subject: [PATCH 053/722] add icc/ifort/impi/imkl easyconfigs for intel/2016.02 + HPL as testcase --- .../h/HPL/HPL-2.1-intel-2016.02.eb | 18 +++++++++ .../i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 34 +++++++++++++++++ .../iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 18 +++++++++ .../ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 34 +++++++++++++++++ .../i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb | 22 +++++++++++ ...11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 38 +++++++++++++++++++ ....181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 34 +++++++++++++++++ 7 files changed, 198 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb new file mode 100644 index 0000000000..f4c0fccb16 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.02'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..f4abc8bef2 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['d6f8529a44231e427219c8e025dec3b2'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..e07e4371a2 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.2.181' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..916145cd26 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..9e93414ff1 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -0,0 +1,22 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.02' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '2.181' +compver = '2016.%s' % suff + +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..74cc4cff3a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.2.181' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-5.3.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..ef29e9af70 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-5.3.0-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' -- GitLab From 4c85cfcbcaf4214827916aa863bfb6425503d90b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 21:21:01 +0000 Subject: [PATCH 054/722] Port to foss-2015b with Perl 5.22.0 --- .../PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb | 118 ++++++++++++++++++ 1 file changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb new file mode 100644 index 0000000000..c5cac8c87f --- /dev/null +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb @@ -0,0 +1,118 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'PRINSEQ' +version = '0.20.4' + +homepage = 'http://prinseq.sourceforge.net' +description = """A bioinformatics tool to PRe-process and show INformation of SEQuence data.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] +sources = ['%(namelower)s-lite-%(version)s.tar.gz'] + +perl = 'Perl' +perlver = '5.22.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::Depends', '0.405', { + 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('ExtUtils::PkgConfig', '1.15', { + 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], + }), + ('Pod::Usage', '1.68', { + 'source_tmpl': 'Pod-Usage-1.68.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + }), + ('File::Temp', '0.2304', { + 'source_tmpl': 'File-Temp-0.2304.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Digest::MD5', '2.54', { + 'source_tmpl': 'Digest-MD5-2.54.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/'], + }), + ('Cairo', '1.106', { + 'source_tmpl': 'Cairo-1.106.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + }), + ('Statistics::PCA', '0.0.1', { + 'source_tmpl': 'Statistics-PCA-0.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSTH/'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-3.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Math::Cephes::Matrix', '0.5304', { + 'source_tmpl': 'Math-Cephes-0.5304.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + }), + ('Math::MatrixReal', '2.12', { + 'source_tmpl': 'Math-MatrixReal-2.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LETO/'], + }), + ('Text::SimpleTable', '2.03', { + 'source_tmpl': 'Text-SimpleTable-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRAMBERG/'], + }), + ('Contextual::Return', '0.004008', { + 'source_tmpl': 'Contextual-Return-0.004008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], + }), +] + +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = [('perl', '%(installdir)s/prinseq-graphs.pl')] + +modextrapaths = { + 'PATH': "", # add installation dir to PATH + 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) +} + +postinstallcmds = [ + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + "chmod +x %(installdir)s/*.pl" # add execution permission +] + +sanity_check_paths = { + 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From e3b608a17ab7d1d29ad29f1585ca97e9048ae9c6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 21:23:08 +0000 Subject: [PATCH 055/722] Use bare Perl --- .../p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb index c5cac8c87f..9d69ec6346 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb @@ -23,7 +23,7 @@ perlver = '5.22.0' versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ - (perl, perlver), + (perl, perlver, '-bare'), ] # these are the perl libraries dependencies -- GitLab From 1fd2f757002f308e9a18d8da6607d72be91112fb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 21:55:51 +0000 Subject: [PATCH 056/722] Port TopHat2 to foss-2015b --- .../t/TopHat/TopHat-2.1.1-foss-2015b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb new file mode 100644 index 0000000000..31db65ea57 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.1' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = [ + 'tophat_ictce.patch', + 'tophat-2.0.13-zlib.patch', +] + +dependencies = [ + ('Boost', '1.60.0'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 78dc6d965f6ee331912f3d693fbb044ce7e713db Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 22:03:45 +0000 Subject: [PATCH 057/722] Disable obsolete bundled SeqAn patch for ictce --- easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb index 31db65ea57..dfc3160664 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb @@ -20,7 +20,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] patches = [ - 'tophat_ictce.patch', + #'tophat_ictce.patch', 'tophat-2.0.13-zlib.patch', ] -- GitLab From 2a49fc45bee7a42924637dc5db55c101d5081b91 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 22:06:27 +0000 Subject: [PATCH 058/722] Remove reference to obsolete patch --- easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb index dfc3160664..3bdcb05552 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb @@ -20,7 +20,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] patches = [ - #'tophat_ictce.patch', 'tophat-2.0.13-zlib.patch', ] -- GitLab From 706d522e108ed3af7d674ac1bb113b427cca4a18 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 22:58:56 +0000 Subject: [PATCH 059/722] Port Exonerate to foss-2015b --- .../e/Exonerate/Exonerate-2.2.0-foss-2015b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb new file mode 100644 index 0000000000..56718e16b7 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.2.0' + +homepage = 'http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('GLib', '2.34.3')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' -- GitLab From f3d74231e0f1cb067f670ada15b04c1b3bc167ee Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Feb 2016 08:14:15 +0000 Subject: [PATCH 060/722] Add GLib-2.34.3 for foss-2015b, dep of Exonerate --- .../g/GLib/GLib-2.34.3-foss-2015b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb new file mode 100644 index 0000000000..7b323a630d --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.34.3' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.0.13'), + ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), +] +builddependencies = [('Python', '2.7.3')] + +moduleclass = 'vis' -- GitLab From 5696614ee4628512d461fd548e76d172f013c2fc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Feb 2016 08:21:31 +0000 Subject: [PATCH 061/722] Add gettext 0.18.2 for foss-2015b, required by Exonerate --- .../g/gettext/gettext-0.18.2-foss-2015b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb new file mode 100644 index 0000000000..e7d30bfac7 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.18.2' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' -- GitLab From 16dff43802386b1e30413b192c45ba9ad28c6da9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Feb 2016 08:27:30 +0000 Subject: [PATCH 062/722] Add libxml2 2.9.1 for foss-2015b, required by Exonerate --- .../l/libxml2/libxml2-2.9.1-foss-2015b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb new file mode 100644 index 0000000000..03c075bd1a --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' -- GitLab From 39cce5364c3d11f2fe5beb6d4df0b7b9a217156e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Feb 2016 08:31:24 +0000 Subject: [PATCH 063/722] Add libreadline-6.2 & Python-2.7.3 for foss-2015b, required by Exonerate --- .../libreadline/libreadline-6.2-foss-2015b.eb | 30 ++++++ .../p/Python/Python-2.7.3-foss-2015b.eb | 91 +++++++++++++++++++ 2 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb new file mode 100644 index 0000000000..6589e3ba7c --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.2' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb new file mode 100644 index 0000000000..7bff359058 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb @@ -0,0 +1,91 @@ +name = 'Python' +version = '2.7.3' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.6.1' +scipyversion = '0.10.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), + # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +exts_list = [ + ('setuptools', '0.6c11', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('mpi4py', '1.3', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.17.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.1', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '1.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.12.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), +] + +moduleclass = 'lang' -- GitLab From 9d482c5f629fd622429a12205cc78e75481f2823 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Feb 2016 09:12:02 +0000 Subject: [PATCH 064/722] Fix source location for Exonerate --- easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb index 56718e16b7..6a9d4b5398 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb @@ -17,7 +17,7 @@ description = """ Exonerate is a generic tool for pairwise sequence comparison. toolchain = {'name': 'foss', 'version': '2015b'} -source_urls = [homepage] +source_urls = ['http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [('GLib', '2.34.3')] -- GitLab From 9615ed7316f14d2de87e1c4eb2be54a01236071a Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Mon, 29 Feb 2016 14:44:13 +0100 Subject: [PATCH 065/722] Add easyconfig for latest MVAPICH2 2.1 and 2.2b --- .../m/MVAPICH2/MVAPICH2-2.1-GCC-4.9.3-2.25.eb | 17 +++++++++++++++++ .../m/MVAPICH2/MVAPICH2-2.2b-GCC-4.9.3-2.25.eb | 17 +++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.1-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.2b-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.1-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.1-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..13f9a5a43d --- /dev/null +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.1-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +name = 'MVAPICH2' +version = '2.1' + +homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' +description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH." + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/'] +sources = [SOURCELOWER_TAR_GZ] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['0095ceecb19bbb7fb262131cb9c2cdd6'] + +builddependencies = [('Bison', '3.0.4')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.2b-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.2b-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..7f35d9ebdf --- /dev/null +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.2b-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +name = 'MVAPICH2' +version = '2.2b' + +homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' +description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH." + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/'] +sources = [SOURCELOWER_TAR_GZ] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['5651e8b7a72d7c77ca68da48f3a5d108'] + +builddependencies = [('Bison', '3.0.4')] + +moduleclass = 'mpi' -- GitLab From 59b3ad2fd4b84df9d337f8ec5e1b94dcb7dbaf40 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Mon, 29 Feb 2016 14:57:59 +0100 Subject: [PATCH 066/722] Add new toolchain foos_mv2 2016a Same as foss 2016a except that OpenMPI is replaced by MVAPICH2. --- .../b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb | 22 ++++++++++++ .../f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb | 34 ++++++++++++++++++ .../easyconfigs/f/foss_mv2/foss_mv2-2016a.eb | 35 +++++++++++++++++++ .../g/gmvapich2/gmvapich2-2016a.eb | 25 +++++++++++++ ...ich2-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb | 25 +++++++++++++ 5 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb create mode 100644 easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb create mode 100644 easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..570b1b1c8b --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb new file mode 100644 index 0000000000..757b5eba91 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gmvapich2', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb b/easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb new file mode 100644 index 0000000000..868fa56f62 --- /dev/null +++ b/easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss_mv2' +version = '2016a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + MVAPICH2 for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.3-2.25' + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gmvapich2' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('MVAPICH2', '2.2b', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb new file mode 100644 index 0000000000..efd6351300 --- /dev/null +++ b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb @@ -0,0 +1,25 @@ +easyblock = "Toolchain" + +name = 'gmvapich2' +version = '2016a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including MVAPICH2 for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.9.3-2.25' +comp = (compname, compver) + +mpilib = 'MVAPICH2' +mpiver = '2.2b' + +# compiler toolchain dependencies +dependencies = [ + comp, + (mpilib, mpiver, '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..ea5206c7ec --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gmvapich2', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blassuff = '-LAPACK-3.6.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.3-2.25'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From cf8af929948aab0e69ac63c4a69a2ca95d097779 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 18:31:30 +0100 Subject: [PATCH 067/722] {numlib}[intel/2016a] CGAL 4.7 (WIP) --- .../CGAL-4.7-intel-2016a-Python-2.7.11.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1e7bf4a653 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['623d91fb2ab0a35049dc6098a0f235cc'] + + +mesaver = '11.1.2' +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('MPFR', '3.1.3', '-GMP-6.1.0'), + ('Qt5', '5.5.1', '-Mesa-%s' % mesaver), + ('Mesa', mesaver, versionsuffix), + ('libGLU', '9.0.0', '-Mesa-%s' % mesaver), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.4.1'), +] + +moduleclass = 'numlib' -- GitLab From a13cd4a58ec6afa53a1a94456cde5b0132321982 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 19:56:21 +0100 Subject: [PATCH 068/722] fix binutils version in M4 easyconfig --- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb index 0a925c97ef..434b6f02ff 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.26', '', True)] configopts = "--enable-cxx" -- GitLab From 56f9e64c25579bf780f1673462c44839ef9b62ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 19:57:44 +0100 Subject: [PATCH 069/722] fix source URL for GCC tarball in GCCcore easyconfig --- easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index e7aac86863..1f2fc04edb 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.3' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official -- GitLab From adbae798a1cb89db32c3a047537bb6f2318ae7c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 20:17:02 +0100 Subject: [PATCH 070/722] add clarifying comment --- easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/icc/icc-2016.0.109.eb | 1 + easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 1 + 8 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 7354472c7e..17d0ffe45a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index c6144a5afd..e56edba4db 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -12,6 +12,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] checksums = ['f57a892fb494db3c80f20a88aa3e901f'] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index 0748e2d400..d80f4b798c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index f4abc8bef2..080cfccc9a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index c188753ac5..b41f57ab66 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index b01714a6f5..c64470205a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -12,6 +12,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tg checksums = ['bce7f6a71f7e44f67956197501d00b7c'] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index f961cef224..4e5be0a9bb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 916145cd26..3ee926155e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -- GitLab From f1ea4e405247379130399eecb2ea64b88ad2ef1a Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 1 Mar 2016 14:39:31 +0100 Subject: [PATCH 071/722] Rename foss_mv2/2016a to gmvolf/2016a --- .../{f/foss_mv2/foss_mv2-2016a.eb => g/gmvolf/gmvolf-2016a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/{f/foss_mv2/foss_mv2-2016a.eb => g/gmvolf/gmvolf-2016a.eb} (98%) diff --git a/easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb b/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb similarity index 98% rename from easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb rename to easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb index 868fa56f62..b9a63b2c7c 100644 --- a/easybuild/easyconfigs/f/foss_mv2/foss_mv2-2016a.eb +++ b/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'Toolchain' -name = 'foss_mv2' +name = 'gmvolf' version = '2016a' homepage = '(none)' -- GitLab From 41d4edb4448ceed6054e0ec90e1f016dcbc6257a Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 1 Mar 2016 14:52:20 +0100 Subject: [PATCH 072/722] Add new toolchain gmpolf/2016a (same as foss/2016a but with MPICH 3.2) --- .../f/FFTW/FFTW-3.3.4-gmpich-2016a.eb | 34 ++++++++++++++++++ .../easyconfigs/g/gmpich/gmpich-2016a.eb | 25 +++++++++++++ .../easyconfigs/g/gmpolf/gmpolf-2016a.eb | 35 +++++++++++++++++++ .../m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb | 16 +++++++++ ...pich-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb | 25 +++++++++++++ 5 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmpich-2016a.eb create mode 100644 easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb create mode 100644 easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb create mode 100644 easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmpich-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmpich-2016a.eb new file mode 100644 index 0000000000..71efac9c7e --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmpich-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gmpich', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb new file mode 100644 index 0000000000..d495830401 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb @@ -0,0 +1,25 @@ +easyblock = "Toolchain" + +name = 'gmpich' +version = '2016a' + +homepage = '(none)' +description = """gcc and GFortran based compiler toolchain, + including MPICH for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.9.3-2.25' +comp = (compname, compver) + +mpilib = 'MPICH' +mpiver = '3.2' + +# compiler toolchain dependencies +dependencies = [ + comp, + (mpilib, mpiver, '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb new file mode 100644 index 0000000000..391d1f7f0c --- /dev/null +++ b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb @@ -0,0 +1,35 @@ +easyblock = "Toolchain" + +name = 'gmpolf' +version = '2016a' + +homepage = '(none)' +description = """gcc and GFortran based compiler toolchain, + MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.3-2.25' + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gmpich' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('MVAPICH2', '2.2b', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..06251f71e8 --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,16 @@ +name = 'MPICH' +version = '3.2' + +homepage = 'http://www.mpich.org/' +description = """MPICH v3.x is an open source high-performance MPI 3.0 implementation. +It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.mpich.org/static/tarballs/%(version)s'] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['f414cfa77099cd1fa1a5ae4e22db508a'] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..9cf751a2ad --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gmpich', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blassuff = '-LAPACK-3.6.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.3-2.25'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 85f5c7e0dab202958c57ad7cb10fb67f786c8aa0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 1 Mar 2016 17:13:24 +0000 Subject: [PATCH 073/722] Bump Python dep of GLib to 2.7.11 --- easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb index 7b323a630d..9226838fbe 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb @@ -17,6 +17,6 @@ dependencies = [ ('gettext', '0.18.2'), ('libxml2', '2.9.1'), ] -builddependencies = [('Python', '2.7.3')] +builddependencies = [('Python', '2.7.11')] moduleclass = 'vis' -- GitLab From 43be742f7950497b92e6004429e1505b6e7b7ab3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 1 Mar 2016 17:39:51 +0000 Subject: [PATCH 074/722] Fix GLib Python dep to 2.7.10 --- easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb index 9226838fbe..04873f8e5c 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-foss-2015b.eb @@ -17,6 +17,6 @@ dependencies = [ ('gettext', '0.18.2'), ('libxml2', '2.9.1'), ] -builddependencies = [('Python', '2.7.11')] +builddependencies = [('Python', '2.7.10')] moduleclass = 'vis' -- GitLab From 6d09160f4ab0a0189093278d00998be5eeb280dc Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 1 Mar 2016 18:41:10 +0100 Subject: [PATCH 075/722] Remove explicit ConfigureMake in MPICH easyconfig because it now has its own easyblock --- easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb | 2 -- easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb index ecc1ac4836..971d6adf6f 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'MPICH' version = '3.0.3' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb index f81230a16b..1b8044cecf 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'MPICH' version = '3.0.4' -- GitLab From daa3272710f05a34d76e94a6b3941c1215a1422a Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 1 Mar 2016 20:26:02 +0100 Subject: [PATCH 076/722] Update MPICH easyconfig files --- .../m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb | 16 +++------------- .../m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb | 17 +++-------------- 2 files changed, 6 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb index 971d6adf6f..e96f02635c 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb @@ -8,19 +8,9 @@ It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).""" toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.mpich.org/static/tarballs/%s' % version] +source_urls = ['http://www.mpich.org/static/tarballs/%(version)s'] -# MPICH configure wants F90/F90FLAGS to be renamed to FC/FCFLAGS. -preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset F90FLAGS; ' - -# Build shared libraries -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', - 'bin/mpiexec', 'bin/mpirun', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h'], - 'dirs': [], -} +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['ee2b8a8b88e3915804df0efcc747c48b'] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb index 1b8044cecf..cf4928e564 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.0.4-GCC-4.8.1.eb @@ -7,21 +7,10 @@ It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).""" toolchain = {'name': 'GCC', 'version': '4.8.1'} -sources = ['mpich-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.mpich.org/static/tarballs/%(version)s'] -# MPICH configure wants F90/F90FLAGS to be renamed to FC/FCFLAGS. -preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset F90FLAGS; ' - -# Build shared libraries -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', 'bin/mpiexec', 'bin/mpirun', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', 'lib/libfmpich.a', 'lib/libfmpich.%s' % SHLIB_EXT, - 'lib/libmpich.a', 'lib/libmpich.%s' % SHLIB_EXT, 'lib/libmpichcxx.a', 'lib/libmpichcxx.%s' % SHLIB_EXT, 'lib/libmpichf90.a', - 'lib/libmpichf90.%s' % SHLIB_EXT], - 'dirs': [], -} +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['9c5d5d4fe1e17dd12153f40bc5b6dbc0'] moduleclass = 'mpi' -- GitLab From 7fd15a76581d533a36e0320a545bd267fb9a6eac Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Wed, 2 Mar 2016 18:23:21 +0100 Subject: [PATCH 077/722] Updated psmpi easyconfig files to use the new psmpi easyblock --- .../easyconfigs/p/pscom/pscom-5.0.48-1.eb | 23 ++++++++++++ .../p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 37 +++++++------------ .../psmpi-5.1.0-1-iccifort-2015.1.133.eb | 28 +++----------- .../p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb | 27 ++++++++++++++ .../psmpi-5.1.5-1-iccifort-2015.1.133.eb | 27 ++++++++++++++ 5 files changed, 95 insertions(+), 47 deletions(-) create mode 100644 easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb create mode 100644 easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb create mode 100644 easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb new file mode 100644 index 0000000000..13b9a47c54 --- /dev/null +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'pscom' +version = '5.0.48-1' + +homepage = 'http://www.par-tec.com' +description = "ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer." + +toolchain = {'version': '', 'name': 'dummy'} + +sources = ['%(version)s.zip'] +source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] + +builddependencies = [ + ('popt', '1.16'), +] + +sanity_check_paths = { + 'files': ['include/%(name)s.h', ('lib/libpscom.so', 'lib64/libpscom.so'), ('lib/libpscom4mxm.so', 'lib64/libpscom4mxm.so')], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 3e04c7775f..87539a2e7d 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -1,13 +1,15 @@ -easyblock = 'ConfigureMake' - name = 'psmpi' version = '5.1.0-1' homepage = 'https://github.com/ParaStation/psmpi2' -description = """ParaStation MPI as part of the ParaStationV5 cluster suite provides robust, flexible and scalable communication and management functions for Linux-based compute clusters. Beside parallel applications based on the Message Passing Interface specification, version 2 (MPI2), also serial applications are supported.""" - +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'defaultopt': True} + sources = [ '%(version)s.tar.gz', 'openpa-1.0.4.tar.gz', @@ -17,26 +19,13 @@ source_urls = [ 'https://trac.mpich.org/projects/openpa/raw-attachment/wiki/Downloads/', ] -# MPICH configure wants F90/F90FLAGS to be renamed to FC/FCFLAGS. -preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset F90FLAGS; ' - -# Build shared libraries -configopts = '--with-confset=gcc --enable-shared --enable-static' - -dependencies = [('pscom', '5.0.44-1')] +dependencies = [ + ('pscom', '5.0.44-1', '', True), +] -sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', - ('lib/libfmpich.a', 'lib64/libfmpich.a'), - ('lib/libfmpich.%s' % SHLIB_EXT, 'lib64/libfmpich.%s' % SHLIB_EXT), - ('lib/libmpich.a', 'lib64/libmpich.a'), - ('lib/libmpich.%s' % SHLIB_EXT, 'lib64/libmpich.%s' % SHLIB_EXT), - ('lib/libmpichcxx.a', 'lib64/libmpichcxx.a'), - ('lib/libmpichcxx.%s' % SHLIB_EXT, 'lib64/libmpichcxx.%s' % SHLIB_EXT), - ('lib/libmpichf90.a', 'lib64/libmpichf90.a'), - ('lib/libmpichf90.%s' % SHLIB_EXT, 'lib64/libmpichf90.%s' % SHLIB_EXT)], - 'dirs': [], -} +hiddendependencies = [ + ('pscom', '5.0.44-1', '', True), +] +configopts = '--with-confset=gcc PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index 4bb1ff6f7a..a57afdf688 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -1,11 +1,11 @@ -easyblock = 'ConfigureMake' - name = 'psmpi' version = '5.1.0-1' homepage = 'https://github.com/ParaStation/psmpi2' -description = """ParaStation MPI as part of the ParaStationV5 cluster suite provides robust, flexible and scalable communication and management functions for Linux-based compute clusters. Beside parallel applications based on the Message Passing Interface specification, version 2 (MPI2), also serial applications are supported.""" - +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" toolchain = {'name': 'iccifort', 'version': '2015.1.133'} sources = [ @@ -17,26 +17,8 @@ source_urls = [ 'https://trac.mpich.org/projects/openpa/attachment/wiki/Downloads', ] -# MPICH configure wants F90/F90FLAGS to be renamed to FC/FCFLAGS. -preconfigopts = 'export FC="$F90"; export FCFLAGS="$F90FLAGS"; unset F90; unset F90FLAGS; ' - -# Build shared libraries -configopts = '--with-confset=intel --enable-shared --enable-static --enable-romio --enable-mpe' +configopts = '--with-confset=intel' dependencies = [('pscom', '5.0.44-1')] -sanity_check_paths = { - 'files': ['bin/mpicc', 'bin/mpicxx', 'bin/mpic++', 'bin/mpif77', 'bin/mpif90', - 'include/mpi.h', 'include/mpi.mod', 'include/mpif.h', - ('lib/libfmpich.a', 'lib64/libfmpich.a'), - ('lib/libfmpich.%s' % SHLIB_EXT, 'lib64/libfmpich.%s' % SHLIB_EXT), - ('lib/libmpich.a', 'lib64/libmpich.a'), - ('lib/libmpich.%s' % SHLIB_EXT, 'lib64/libmpich.%s' % SHLIB_EXT), - ('lib/libmpichcxx.a', 'lib64/libmpichcxx.a'), - ('lib/libmpichcxx.%s' % SHLIB_EXT, 'lib64/libmpichcxx.%s' % SHLIB_EXT), - ('lib/libmpichf90.a', 'lib64/libmpichf90.a'), - ('lib/libmpichf90.%s' % SHLIB_EXT, 'lib64/libmpichf90.%s' % SHLIB_EXT)], - 'dirs': [], -} - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb new file mode 100644 index 0000000000..b7c5d500a2 --- /dev/null +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb @@ -0,0 +1,27 @@ +name = 'psmpi' +version = '5.1.5-1' + +homepage = 'https://github.com/ParaStation/psmpi2' +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" + +toolchain = {'version': '4.9.3', 'name': 'GCC'} + +toolchainopts = {'defaultopt': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] + +dependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +hiddendependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +configopts = ' --with-confset=gcc PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb new file mode 100644 index 0000000000..92f6033fa8 --- /dev/null +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb @@ -0,0 +1,27 @@ +name = 'psmpi' +version = '5.1.5-1' + +homepage = 'https://github.com/ParaStation/psmpi2' +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" + +toolchain = {'version': '2015.1.133', 'name': 'iccifort'} + +toolchainopts = {'defaultopt': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] + +dependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +hiddendependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +configopts = ' --with-confset=intel PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' + +moduleclass = 'mpi' -- GitLab From 861f5a1e81be0a986ff0f31a27762ca148c61852 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Wed, 2 Mar 2016 18:29:44 +0100 Subject: [PATCH 078/722] Small fixes --- .../easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 3 +-- .../p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb | 10 ++++++++-- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 87539a2e7d..34f4d57dd7 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -8,8 +8,6 @@ various batch systems for tighter process control. """ toolchain = {'name': 'GCC', 'version': '4.9.2'} -toolchainopts = {'defaultopt': True} - sources = [ '%(version)s.tar.gz', 'openpa-1.0.4.tar.gz', @@ -26,6 +24,7 @@ dependencies = [ hiddendependencies = [ ('pscom', '5.0.44-1', '', True), ] + configopts = '--with-confset=gcc PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index a57afdf688..ac08d5c585 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -17,8 +17,14 @@ source_urls = [ 'https://trac.mpich.org/projects/openpa/attachment/wiki/Downloads', ] -configopts = '--with-confset=intel' +dependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +hiddendependencies = [ + ('pscom', '5.0.48-1', '', True), +] -dependencies = [('pscom', '5.0.44-1')] +configopts = '--with-confset=intel PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' moduleclass = 'mpi' -- GitLab From 42f838992f1526a957c91a6f05161466394b3636 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 18:43:11 +0100 Subject: [PATCH 079/722] rename to intel/2016.02-GCC-5.3 --- ...1-intel-2016.02.eb => HPL-2.1-intel-2016.02-GCC-5.3.eb} | 2 +- .../i/intel/{intel-2016.02.eb => intel-2016.02-GCC-5.3.eb} | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/h/HPL/{HPL-2.1-intel-2016.02.eb => HPL-2.1-intel-2016.02-GCC-5.3.eb} (91%) rename easybuild/easyconfigs/i/intel/{intel-2016.02.eb => intel-2016.02-GCC-5.3.eb} (85%) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb similarity index 91% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb index f4c0fccb16..ffa453cdb4 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'intel', 'version': '2016.02'} +toolchain = {'name': 'intel', 'version': '2016.02-GCC-5.3'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb similarity index 85% rename from easybuild/easyconfigs/i/intel/intel-2016.02.eb rename to easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb index 47932a57f9..4d1e0dddac 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb @@ -1,8 +1,9 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild -easyblock = "Toolchain" +easyblock = 'Toolchain' name = 'intel' version = '2016.02' +gcc_maj_min = '5.3' +versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" @@ -10,7 +11,7 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.2.181' -gccver = '5.3.0' +gccver = '%s.0' % gcc_maj_min binutilsver = '2.26' gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ -- GitLab From 0886e5027a7736285c13f867627a2a8673d9a4cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 19:57:33 +0200 Subject: [PATCH 080/722] add easyconfig HPL-2.1-intel-2016.02-GCC-4.9.eb, add easyconfig binutils-2.26-GCCcore-4.9.3.eb, add easyconfig flex-2.6.0-GCCcore-4.9.3.eb, add easyconfig icc-2016.2.181-GCC-4.9.3-2.26.eb, add easyconfig iccifort-2016.2.181-GCC-4.9.3-2.26.eb, add easyconfig ifort-2016.2.181-GCC-4.9.3-2.26.eb, add easyconfig iimpi-2016.02-GCC-4.9.3-2.26.eb, add easyconfig imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb, add easyconfig impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb, add easyconfig intel-2016.02-GCC-4.9.eb --- .../b/binutils/binutils-2.26-GCCcore-4.9.3.eb | 41 +++++++++++++++++++ .../f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 21 ++++++++++ .../h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb | 18 ++++++++ .../i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb | 35 ++++++++++++++++ .../iccifort-2016.2.181-GCC-4.9.3-2.26.eb | 18 ++++++++ .../ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb | 35 ++++++++++++++++ .../i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb | 22 ++++++++++ ...11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb | 38 +++++++++++++++++ ....181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb | 34 +++++++++++++++ .../i/intel/intel-2016.02-GCC-4.9.eb | 26 ++++++++++++ 10 files changed, 288 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..0d3fdd2d17 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..5a3de111fc --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -0,0 +1,21 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +parallel = 1 + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..977c7d487d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..ec73b70b03 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['d6f8529a44231e427219c8e025dec3b2'] + +gccver = '4.9.3' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..93577bed54 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.2.181' +versionsuffix = '-GCC-4.9.3-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..c55e928942 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] + +gccver = '4.9.3' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..0be81ea753 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb @@ -0,0 +1,22 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.02' +versionsuffix = '-GCC-4.9.3-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '2.181' +compver = '2016.%s' % suff + +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..78baf11191 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.2.181' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-4.9.3-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb new file mode 100644 index 0000000000..147e9c1ec1 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-4.9.3-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..955db91710 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.02' +gcc_maj_min = '4.9' +versionsuffix = '-GCC-%s' % gcc_maj_min + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.2.181' +gccver = '%s.3' % gcc_maj_min +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.2.181', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' -- GitLab From 6cc138ca5ec6cd4aaea6917159a494a892746d8a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 2 Mar 2016 17:59:17 +0000 Subject: [PATCH 081/722] Use existing non-bare Perl 5.20.3 --- ...erl-5.22.0.eb => PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/PRINSEQ/{PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb => PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb} (98%) diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb similarity index 98% rename from easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb rename to easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb index 9d69ec6346..1d36878e90 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.22.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb @@ -19,11 +19,11 @@ source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] sources = ['%(namelower)s-lite-%(version)s.tar.gz'] perl = 'Perl' -perlver = '5.22.0' +perlver = '5.20.3' versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ - (perl, perlver, '-bare'), + (perl, perlver), ] # these are the perl libraries dependencies -- GitLab From b8e4a25cec60fe50c037e9614ac6d497a916b47e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 2 Mar 2016 18:09:15 +0000 Subject: [PATCH 082/722] First version of Subread --- .../s/Subread/Subread-1.5.0p1-foss-2015b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb new file mode 100644 index 0000000000..245a7b2f5a --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb @@ -0,0 +1,30 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# It was auto-generated based on a template easyconfig, so it should be used with care. +easyblock = 'MakeCp' + +name = 'Subread' +version = '1.5.0p1' + +homepage = 'http://subread.sourceforge.net/' +description = """TEMPLATE DESCRIPTION""" + +# toolchain name should be 'TEMPLATE' if this is a template, so EasyBuild knows and is willing to use it as a template +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... + +# For sources line to work correctly with --try-software-version, you MUST employ %s OR use a construct like SOURCE_TAR_GZ +sources = ['%(namelower)s-%version)s-source.tar.gz'] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [] + +dependencies = [] + +# The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From f038794ebafd3137021e07532136e6b116b631ce Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 2 Mar 2016 21:43:15 +0000 Subject: [PATCH 083/722] Add first draft of RSeQC including numpy dep --- .../numpy-1.9.2-foss-2015b-Python-2.7.10.eb | 27 ++++++++++++++ .../r/RSeQC/RSeQC-2.6.3-foss-2015b.eb | 35 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..f55df325cf --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,27 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SuiteSparse', '4.4.5', '-METIS-5.1.0'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb new file mode 100644 index 0000000000..c0f1f917f6 --- /dev/null +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'RSeQC' +version = '2.6.3' + +homepage = 'http://rseqc.sourceforge.net/' +description = """RSeQC provides a number of useful modules that can + comprehensively evaluate high throughput sequence data especially RNA-seq + data. Some basic modules quickly inspect sequence quality, nucleotide + composition bias, PCR bias and GC bias, while RNA-seq specific modules + evaluate sequencing saturation, mapped reads distribution, coverage + uniformity, strand specificity, transcript level RNA integrity etc.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [] + +Python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + ('R', '3.2.3'), + ('numpy', '1.9.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From cadbf9619dacee2b0df04dc31a4712631e483c00 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 3 Mar 2016 13:57:19 +0100 Subject: [PATCH 084/722] Use directly '--with-mpe' configopt for MVAPICH2 1.7 instead of to-be-removed 'withmpe' from MVAPICH2 EB --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index cee59253ac..8208f0a521 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -15,7 +15,7 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] rdma_type = "gen2" # 'gen2' or 'udapl' # enable building of MPE routines -withmpe = True +configopts = '--with-mpe ' # enable hwloc support withhwloc = True diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb index 22a7f9f02e..429ab72ae0 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb @@ -16,7 +16,7 @@ builddependencies = [('Bison', '2.5')] rdma_type = "gen2" # 'gen2' or 'udapl' # enable building of MPE routines -withmpe = True +configopts = '--with-mpe ' # parallel build tends to fail parallel = 1 -- GitLab From 6db12d99703e23e76336abbe58be66dee5b71902 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 3 Mar 2016 13:57:41 +0100 Subject: [PATCH 085/722] Use directly '--with-hwloc' configopt for MVAPICH2 1.7 instead of to-be-removed 'withhwloc' from MVAPICH2 EB --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 8208f0a521..7f3c50d87a 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -18,7 +18,7 @@ rdma_type = "gen2" # 'gen2' or 'udapl' configopts = '--with-mpe ' # enable hwloc support -withhwloc = True +configopts += '--with-hwloc ' dependencies = [('hwloc', '1.5.1')] # enable checkpointing support -- GitLab From 0f56d11a401e34e1a91890dee825e1da94a1c984 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 3 Mar 2016 14:08:23 +0100 Subject: [PATCH 086/722] Remove option rdma_type = "gen2" because it is actually the default This makes this EasyConfig files more uniform with the recent ones --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 -- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 7f3c50d87a..137b9059fe 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -12,8 +12,6 @@ sources = [SOURCELOWER_TGZ] # note: this URL will only work for the most recent version (previous versions no longer available?) source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] -rdma_type = "gen2" # 'gen2' or 'udapl' - # enable building of MPE routines configopts = '--with-mpe ' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb index 429ab72ae0..4c2eead91f 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb @@ -13,8 +13,6 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] builddependencies = [('Bison', '2.5')] -rdma_type = "gen2" # 'gen2' or 'udapl' - # enable building of MPE routines configopts = '--with-mpe ' -- GitLab From d2e3b5810c31a9d9e155587647dc3459588f9df4 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 3 Mar 2016 14:11:07 +0100 Subject: [PATCH 087/722] Add checksum if known --- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb | 3 +++ .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb | 3 +++ .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb | 3 +++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb | 3 +++ .../m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb | 3 +++ 5 files changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb index 9be4dedbf3..dbf130a107 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb @@ -9,6 +9,9 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['ef4ae05e3b5ad485326505db7381246c'] + builddependencies = [('Bison', '2.7')] # parallel build doesn't work diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb index 6d98d3a032..f8ed601fa4 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb @@ -9,6 +9,9 @@ toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['5dc58ed08fd3142c260b70fe297e127c'] + dependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb index e1fdfb364f..ec3097f101 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb @@ -9,6 +9,9 @@ toolchain = {'name': 'ClangGCC', 'version': '1.2.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['5dc58ed08fd3142c260b70fe297e127c'] + dependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb index 602d1c4c80..fc82223d21 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb @@ -9,6 +9,9 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['5dc58ed08fd3142c260b70fe297e127c'] + builddependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb index f87ce5fafe..2ff528acce 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb @@ -10,6 +10,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['5dc58ed08fd3142c260b70fe297e127c'] + builddependencies = [('Bison', '2.7')] # the hydra launcher start's before LD_LIBRARY_PATH is forwarded, so we provide this hint on where to find some libs -- GitLab From c0b90b90ff6dc24a40e0d5f148dced00cd393875 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 3 Mar 2016 14:58:16 +0100 Subject: [PATCH 088/722] Enhanced easyconfigs that need the new psmpi.py easyblock --- .../p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 4 +-- .../psmpi-5.1.0-1-iccifort-2015.1.133.eb | 4 +-- .../p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb | 30 +++++++++++++++++++ .../p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb | 4 +-- .../psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb | 30 +++++++++++++++++++ .../psmpi-5.1.5-1-iccifort-2015.1.133.eb | 4 +-- 6 files changed, 68 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb create mode 100644 easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 34f4d57dd7..3b8d70635f 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -17,6 +17,8 @@ source_urls = [ 'https://trac.mpich.org/projects/openpa/raw-attachment/wiki/Downloads/', ] +mpich_opts = '--enable-static' + dependencies = [ ('pscom', '5.0.44-1', '', True), ] @@ -25,6 +27,4 @@ hiddendependencies = [ ('pscom', '5.0.44-1', '', True), ] -configopts = '--with-confset=gcc PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index ac08d5c585..a5c1e058f0 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -17,6 +17,8 @@ source_urls = [ 'https://trac.mpich.org/projects/openpa/attachment/wiki/Downloads', ] +mpich_opts = '--enable-static' + dependencies = [ ('pscom', '5.0.48-1', '', True), ] @@ -25,6 +27,4 @@ hiddendependencies = [ ('pscom', '5.0.48-1', '', True), ] -configopts = '--with-confset=intel PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb new file mode 100644 index 0000000000..c783f37b64 --- /dev/null +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb @@ -0,0 +1,30 @@ +name = 'psmpi' +version = '5.1.5-1' +versionsuffix = '-mt' + +homepage = 'https://github.com/ParaStation/psmpi2' +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" + +toolchain = {'version': '4.9.3', 'name': 'GCC'} + +toolchainopts = {'defaultopt': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] + +mpich_opts = '--enable-static' + +threaded = True + +dependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +hiddendependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb index b7c5d500a2..aac098925c 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb @@ -14,6 +14,8 @@ toolchainopts = {'defaultopt': True} sources = ['%(version)s.tar.gz'] source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] +mpich_opts = '--enable-static' + dependencies = [ ('pscom', '5.0.48-1', '', True), ] @@ -22,6 +24,4 @@ hiddendependencies = [ ('pscom', '5.0.48-1', '', True), ] -configopts = ' --with-confset=gcc PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb new file mode 100644 index 0000000000..c33effaedb --- /dev/null +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb @@ -0,0 +1,30 @@ +name = 'psmpi' +version = '5.1.5-1' +versionsuffix = '-mt' + +homepage = 'https://github.com/ParaStation/psmpi2' +description = """ParaStation MPI is an open source high-performance MPI 3.0 implementation, +based on MPICH v3. It provides extra low level communication libraries and integration with +various batch systems for tighter process control. +""" + +toolchain = {'version': '2015.1.133', 'name': 'iccifort'} + +toolchainopts = {'defaultopt': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] + +mpich_opts = '--enable-static' + +threaded = True + +dependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +hiddendependencies = [ + ('pscom', '5.0.48-1', '', True), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb index 92f6033fa8..22468a4f7f 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb @@ -14,6 +14,8 @@ toolchainopts = {'defaultopt': True} sources = ['%(version)s.tar.gz'] source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] +mpich_opts = '--enable-static' + dependencies = [ ('pscom', '5.0.48-1', '', True), ] @@ -22,6 +24,4 @@ hiddendependencies = [ ('pscom', '5.0.48-1', '', True), ] -configopts = ' --with-confset=intel PSCOM_LDFLAGS=-L$EBROOTPSCOM/lib PSCOM_CPPFLAGS=-I$EBROOTPSCOM/include --with-mpichconf="--enable-static" ' - moduleclass = 'mpi' -- GitLab From 9d202a7e73953c2e17fb64e6476bd3b75edfe3fd Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Fri, 4 Mar 2016 11:45:49 +0100 Subject: [PATCH 089/722] Revert "Use directly '--with-hwloc' configopt for MVAPICH2 1.7 instead of to-be-removed 'withhwloc' from MVAPICH2 EB" This reverts commit 6db12d99703e23e76336abbe58be66dee5b71902. --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 137b9059fe..95bd5200b6 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -16,7 +16,7 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] configopts = '--with-mpe ' # enable hwloc support -configopts += '--with-hwloc ' +withhwloc = True dependencies = [('hwloc', '1.5.1')] # enable checkpointing support -- GitLab From 43112ab3f8c4fe9e7c9cf9dce36fb392ac6fd1c3 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Fri, 4 Mar 2016 11:45:55 +0100 Subject: [PATCH 090/722] Revert "Use directly '--with-mpe' configopt for MVAPICH2 1.7 instead of to-be-removed 'withmpe' from MVAPICH2 EB" This reverts commit cadbf9619dacee2b0df04dc31a4712631e483c00. --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 95bd5200b6..a20b1e03f0 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TGZ] source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] # enable building of MPE routines -configopts = '--with-mpe ' +withmpe = True # enable hwloc support withhwloc = True diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb index 4c2eead91f..76de06e6fd 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb @@ -14,7 +14,7 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] builddependencies = [('Bison', '2.5')] # enable building of MPE routines -configopts = '--with-mpe ' +withmpe = True # parallel build tends to fail parallel = 1 -- GitLab From 08a1f1630b4a92d877a3bc279622d8cc3e7cf102 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Mar 2016 15:56:32 +0100 Subject: [PATCH 091/722] remove custom exts_filter in various easyconfigs for (bundles of) Python packages --- .../i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb | 1 - .../i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb | 1 - .../i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb | 1 - .../m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb | 1 - .../m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb | 1 - .../m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb | 1 - .../n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb | 1 - .../s/Sphinx/Sphinx-1.3.3-intel-2015b-Python-2.7.11.eb | 1 - 8 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb index 4c966b0d8a..92dcaa700c 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb @@ -25,7 +25,6 @@ dependencies = [ # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('pysqlite', '2.7.0', { diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb index 6a2901ff52..693b2889a6 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb @@ -25,7 +25,6 @@ dependencies = [ # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('pysqlite', '2.8.1', { diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb index fd3e839da8..e3341fcf31 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb @@ -25,7 +25,6 @@ dependencies = [ # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('pysqlite', '2.8.1', { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb index 207a23ff90..712519a60c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'foss', 'version': '2015b'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') dependencies = [ ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb index 1364208cee..8b047bb737 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'intel', 'version': '2015b'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') dependencies = [ ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb index c62d74a1eb..551c06ecef 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'intel', 'version': '2016a'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') dependencies = [ ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb index 402bb7ef96..6456ccb4fb 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.22.1-intel-2015b-Python-2.7.11.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'intel', 'version': '2015b'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') pyver = '2.7.11' versionsuffix = '-Python-%s' % pyver diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.3.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.3.3-intel-2015b-Python-2.7.11.eb index 3813e03737..be559f9b42 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.3.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.3.3-intel-2015b-Python-2.7.11.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'intel', 'version': '2015b'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s"', '') pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[0:2]) -- GitLab From 63bb41c84a63bb99714ee6c70e633e6453074961 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 09:35:23 +0100 Subject: [PATCH 092/722] {bio}[intel/2016a] npstat 0.99 --- .../npstat-0.99_fix-hardcoding-Makefile.patch | 16 +++++++++ easybuild/easyconfigs/n/npstat/npstat.eb | 33 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch create mode 100644 easybuild/easyconfigs/n/npstat/npstat.eb diff --git a/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch b/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch new file mode 100644 index 0000000000..b9cdbe3811 --- /dev/null +++ b/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch @@ -0,0 +1,16 @@ +fix hardcoding of 'gcc' +author: Kenneth Hoste (HPC-UGent) +--- npstat/trunk/Makefile.orig 2016-02-15 01:16:51.000000000 +0100 ++++ npstat/trunk/Makefile 2016-03-10 09:25:46.000000000 +0100 +@@ -1,8 +1,7 @@ + all: npstat + +- + npstat: +- gcc -o npstat NPStat-v0.99.c -lgsl -lgslcblas -lm ++ ${CC} -o npstat NPStat-v0.99.c -lgsl -lgslcblas -lm + + clean: +- rm npstat +\ No newline at end of file ++ rm npstat diff --git a/easybuild/easyconfigs/n/npstat/npstat.eb b/easybuild/easyconfigs/n/npstat/npstat.eb new file mode 100644 index 0000000000..b8f9940b59 --- /dev/null +++ b/easybuild/easyconfigs/n/npstat/npstat.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'npstat' +version = '0.99' + +homepage = 'https://code.google.com/archive/p/npstat/' +description = """npstat implements some population genetics tests and estimators that can be applied + to pooled sequences from Next Generation Sequencing experiments.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://storage.googleapis.com/google-code-archive-source/v2/code.google.com/npstat/'] +sources = ['source-archive.zip'] + +patches = ['npstat-%(version)s_fix-hardcoding-Makefile.patch'] + +# commit 14, Oct 31st 2013 +checksums = ['a1595b7c46312d0f51b8b68987289337'] + +dependencies = [ + ('GSL', '1.16'), +] + +start_dir = 'trunk' + +files_to_copy = [(['npstat'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/npstat'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a9cd29fdaa6c1bc62c65738484548ab0dfad6d11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 09:58:56 +0100 Subject: [PATCH 093/722] switch to foss/2016a (& fix easyconfig filename) + fix remarks w.r.t. $CFLAGS in patch --- .../n/npstat/{npstat.eb => npstat-0.99-foss-2016a.eb} | 2 +- .../n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/n/npstat/{npstat.eb => npstat-0.99-foss-2016a.eb} (93%) diff --git a/easybuild/easyconfigs/n/npstat/npstat.eb b/easybuild/easyconfigs/n/npstat/npstat-0.99-foss-2016a.eb similarity index 93% rename from easybuild/easyconfigs/n/npstat/npstat.eb rename to easybuild/easyconfigs/n/npstat/npstat-0.99-foss-2016a.eb index b8f9940b59..b72652fe93 100644 --- a/easybuild/easyconfigs/n/npstat/npstat.eb +++ b/easybuild/easyconfigs/n/npstat/npstat-0.99-foss-2016a.eb @@ -7,7 +7,7 @@ homepage = 'https://code.google.com/archive/p/npstat/' description = """npstat implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments.""" -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://storage.googleapis.com/google-code-archive-source/v2/code.google.com/npstat/'] sources = ['source-archive.zip'] diff --git a/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch b/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch index b9cdbe3811..54420af1c1 100644 --- a/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch +++ b/easybuild/easyconfigs/n/npstat/npstat-0.99_fix-hardcoding-Makefile.patch @@ -1,4 +1,4 @@ -fix hardcoding of 'gcc' +fix hardcoding of 'gcc', add optimization flags defined in $CFLAGS author: Kenneth Hoste (HPC-UGent) --- npstat/trunk/Makefile.orig 2016-02-15 01:16:51.000000000 +0100 +++ npstat/trunk/Makefile 2016-03-10 09:25:46.000000000 +0100 @@ -8,7 +8,7 @@ author: Kenneth Hoste (HPC-UGent) - npstat: - gcc -o npstat NPStat-v0.99.c -lgsl -lgslcblas -lm -+ ${CC} -o npstat NPStat-v0.99.c -lgsl -lgslcblas -lm ++ ${CC} ${CFLAGS} -o npstat NPStat-v0.99.c -lgsl -lgslcblas -lm clean: - rm npstat -- GitLab From 055acbe0dec9d4bc577a6d25cf4cb95601e7144f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 10:27:18 +0100 Subject: [PATCH 094/722] {bio}[foss/2016a] SNAPE-pooled r32 --- .../SNAPE-pooled-r32-foss-2016a.eb | 35 +++++++++++++++++++ ...E-pooled-r32_fix-hardcoding-Makefile.patch | 12 +++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32_fix-hardcoding-Makefile.patch diff --git a/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32-foss-2016a.eb b/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32-foss-2016a.eb new file mode 100644 index 0000000000..ee4b4bad14 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'SNAPE-pooled' +version = 'r32' + +homepage = 'https://code.google.com/archive/p/snape-pooled/' +description = """SNAPE-pooled computes the probability distribution for the frequency of the minor allele + in a certain population, at a certain position in the genome.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://storage.googleapis.com/google-code-archive-source/v2/code.google.com/snape-pooled/'] +sources = ['source-archive.zip'] + +patches = ['SNAPE-pooled-%(version)s_fix-hardcoding-Makefile.patch'] + +# commit 32, Aug 12th 2013 +checksums = ['0e9741a45731a2e92d84c129125db3f1'] + +dependencies = [ + ('OCaml', '4.02.3'), +] + +start_dir = 'trunk' + +buildopts = "snape-pooled snape-pooled-fast" + +files_to_copy = [(['snape-pooled', 'snape-pooled-fast'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/snape-pooled', 'bin/snape-pooled-fast'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32_fix-hardcoding-Makefile.patch b/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32_fix-hardcoding-Makefile.patch new file mode 100644 index 0000000000..85d8d5a910 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-r32_fix-hardcoding-Makefile.patch @@ -0,0 +1,12 @@ +fix hardcoded 'gcc' + add optimization flags through $CFLAGS +author: Kenneth Hoste (HPC-UGent) +--- snape-pooled/trunk/Makefile.orig 2016-03-10 10:23:16.000000000 +0100 ++++ snape-pooled/trunk/Makefile 2016-03-10 10:23:32.000000000 +0100 +@@ -8,6 +8,6 @@ + latex $< + dvips -o snape-pooled-manual.ps snape-pooled-manual.dvi + snape-pooled-fast: snape-pooled.c +- gcc -g -o $@ $< -lm ++ ${CC} ${CFLAGS} -g -o $@ $< -lm + clean: + rm *.cmx *.cmi *.cmo pooled.o snape-pooled *.log *.ps *.dvi *.aux -- GitLab From 3c1a86c564c9ff99c8e7f1f6d755e98b695f2555 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 12:05:22 +0200 Subject: [PATCH 095/722] add easyconfig BWA-0.7.13-foss-2016a.eb, add easyconfig picard-2.1.1-Java-1.8.0_74.eb, add easyconfig GATK-3.5-Java-1.8.0_74.eb --- .../b/BWA/BWA-0.7.13-foss-2016a.eb | 32 +++++++++++++++ .../g/GATK/GATK-3.5-Java-1.8.0_74.eb | 40 +++++++++++++++++++ .../p/picard/picard-2.1.1-Java-1.8.0_74.eb | 18 +++++++++ 3 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb create mode 100644 easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb new file mode 100644 index 0000000000..419aba7bab --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.13 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.13' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb new file mode 100644 index 0000000000..c52824dc92 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '3.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] + +dependencies = [('Java', '1.8.0_74')] + +modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb new file mode 100644 index 0000000000..b7bb2304d4 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb @@ -0,0 +1,18 @@ +name = 'picard' +version = '2.1.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM + (http://samtools.github.io/hts-specs) format.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] +sources = ['%(name)s-tools-%(version)s.zip'] + +dependencies = [('Java', '1.8.0_74')] + +modloadmsg = "To execute picard run: java -jar \\${EBROOTPICARD}/%(name)s.jar" + +moduleclass = 'bio' -- GitLab From c012661d8159a3f76e32fe60a4e36aa035967117 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 10 Mar 2016 11:22:40 +0100 Subject: [PATCH 096/722] Removed hidden deps. Added missing popt easyconfig --- easybuild/easyconfigs/p/popt/popt-1.16.eb | 23 +++++++++++++++++++ .../p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 4 ---- .../psmpi-5.1.0-1-iccifort-2015.1.133.eb | 4 ---- .../p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb | 4 ---- .../p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb | 4 ---- .../psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb | 4 ---- .../psmpi-5.1.5-1-iccifort-2015.1.133.eb | 4 ---- 7 files changed, 23 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/p/popt/popt-1.16.eb diff --git a/easybuild/easyconfigs/p/popt/popt-1.16.eb b/easybuild/easyconfigs/p/popt/popt-1.16.eb new file mode 100644 index 0000000000..4b05ae3e4e --- /dev/null +++ b/easybuild/easyconfigs/p/popt/popt-1.16.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'popt' +version = "1.16" + +homepage = "http://freecode.com/projects/popt" +description = """Popt is a C library for parsing command line parameters.""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://rpm5.org/files/popt/'] +sources = [SOURCE_TAR_GZ] + +toolchainopts = {'optarch': False} +sanity_check_paths = { + 'files': ['include/popt.h', + ('lib/libpopt.a', 'lib64/libpopt.a'), + ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], + 'dirs': [], +} + +maxparallel = 1 + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 3b8d70635f..89eb3c9f54 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -23,8 +23,4 @@ dependencies = [ ('pscom', '5.0.44-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.44-1', '', True), -] - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index a5c1e058f0..e8adea5cdd 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -23,8 +23,4 @@ dependencies = [ ('pscom', '5.0.48-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.48-1', '', True), -] - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb index c783f37b64..1bfdad4fb7 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb @@ -23,8 +23,4 @@ dependencies = [ ('pscom', '5.0.48-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.48-1', '', True), -] - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb index aac098925c..93f76f8af0 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb @@ -20,8 +20,4 @@ dependencies = [ ('pscom', '5.0.48-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.48-1', '', True), -] - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb index c33effaedb..9bf66b5728 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb @@ -23,8 +23,4 @@ dependencies = [ ('pscom', '5.0.48-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.48-1', '', True), -] - moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb index 22468a4f7f..8251dde430 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb @@ -20,8 +20,4 @@ dependencies = [ ('pscom', '5.0.48-1', '', True), ] -hiddendependencies = [ - ('pscom', '5.0.48-1', '', True), -] - moduleclass = 'mpi' -- GitLab From 9183d921acb0e78a46f4ba973e5ec3d4707ce945 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 12:23:12 +0200 Subject: [PATCH 097/722] add easyconfig Perl-5.22.1-foss-2016a.eb --- .../p/Perl/Perl-5.22.1-foss-2016a.eb | 886 ++++++++++++++++++ 1 file changed, 886 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb new file mode 100644 index 0000000000..652f0d5227 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -0,0 +1,886 @@ +name = 'Perl' +version = '5.22.1' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.60', { + 'source_tmpl': 'Config-General-2.60.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.36', { + 'source_tmpl': 'Test-Harness-3.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016020301', { + 'source_tmpl': 'Regexp-Common-2016020301.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-0.026.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.02', { + 'source_tmpl': 'DateTime-Locale-1.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.95', { + 'source_tmpl': 'DateTime-TimeZone-1.95.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4216', { + 'source_tmpl': 'Module-Build-0.4216.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.24', { + 'source_tmpl': 'Try-Tiny-0.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.22', { + 'source_tmpl': 'Params-Validate-1.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.25', { + 'source_tmpl': 'DateTime-1.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.01', { + 'source_tmpl': 'Readonly-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-1.29.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "BINGOS"'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-0.73.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-0.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-3.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.71', { + 'source_tmpl': 'URI-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.44', { + 'source_tmpl': 'Text-Diff-1.44.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.024', { + 'source_tmpl': 'IO-Socket-SSL-2.024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '1.120', { + 'source_tmpl': 'Test-Deep-1.120.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.001001', { + 'source_tmpl': 'Moo-2.001001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.09', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.09.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-0.64.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.15', { + 'source_tmpl': 'Package-DeprecationManager-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "GBARR"'], + }), + ('version', '0.9915', { + 'source_tmpl': 'version-0.9915.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + # fails: uses 'gcc' + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.31', { + 'source_tmpl': 'Time-Piece-1.31.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.12', { + 'source_tmpl': 'AnyEvent-7.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-3.0612.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.15', { + 'source_tmpl': 'libwww-perl-6.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.52', { + 'source_tmpl': 'GDGraph-1.52.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "INGY"'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967013', { + 'source_tmpl': 'Parse-RecDescent-1.967013.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-1.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.33', { + 'source_tmpl': 'XML-XPath-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.36', { + 'source_tmpl': 'Capture-Tiny-0.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000002', { + 'source_tmpl': 'strictures-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.40', { + 'source_tmpl': 'Exception-Class-1.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-2.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.43', { + 'source_tmpl': 'Scalar-List-Utils-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.84', { + 'source_tmpl': 'Log-Handler-0.84.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.01', { + 'source_tmpl': 'Devel-StackTrace-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1605', { + 'source_tmpl': 'Moose-2.1605.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9156', { + 'source_tmpl': 'CPANPLUS-0.9156.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-3.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.18', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-0.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' -- GitLab From 37a39678dd32e9226a54a1ee46a26469c71b1c43 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 10 Mar 2016 12:12:56 +0100 Subject: [PATCH 098/722] Added missing pscom easyconfig --- .../easyconfigs/p/pscom/pscom-5.0.44-1.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb new file mode 100644 index 0000000000..9a9312254f --- /dev/null +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'pscom' +version = '5.0.44-1' +homepage = 'http://www.par-tec.com' +description = """ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] +sources = ['%(version)s.zip'] + +dependencies = [('popt', '1.16')] + + +sanity_check_paths = { + 'files': ['include/pscom.h', ('lib/libpscom.%s' % SHLIB_EXT, 'lib64/libpscom.%s' % SHLIB_EXT)], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 34a2545f7c7cbf88ccbf022a40e0927c70a9cabc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 13:24:13 +0200 Subject: [PATCH 099/722] add easyconfig PHYLIP-3.696-foss-2016a.eb --- .../p/PHYLIP/PHYLIP-3.696-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb new file mode 100644 index 0000000000..090561e4d6 --- /dev/null +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'PHYLIP' +version = '3.696' + +homepage = 'http://evolution.genetics.washington.edu/phylip' +description = "PHYLIP is a free package of programs for inferring phylogenies." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://evolution.gs.washington.edu/phylip/download/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' + +files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.so', 'src/libdrawtree.so'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' -- GitLab From 7d860929075a959ee22e62bc90940dc349531a6b Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 10 Mar 2016 12:27:02 +0100 Subject: [PATCH 100/722] Minor fixed in versioning --- .../easyconfigs/p/pscom/pscom-5.0.44-1.eb | 20 ------------------- .../p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 2 +- 2 files changed, 1 insertion(+), 21 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb deleted file mode 100644 index 9a9312254f..0000000000 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pscom' -version = '5.0.44-1' -homepage = 'http://www.par-tec.com' -description = """ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] -sources = ['%(version)s.zip'] - -dependencies = [('popt', '1.16')] - - -sanity_check_paths = { - 'files': ['include/pscom.h', ('lib/libpscom.%s' % SHLIB_EXT, 'lib64/libpscom.%s' % SHLIB_EXT)], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 89eb3c9f54..dfba4ffaa8 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -20,7 +20,7 @@ source_urls = [ mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.44-1', '', True), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' -- GitLab From 0514fe5162f0f426085766ea037bc54463394c7a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 13:33:36 +0200 Subject: [PATCH 101/722] add easyconfig MUSCLE-3.8.31-intel-2016a.eb --- .../m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb new file mode 100644 index 0000000000..467b83b6ce --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'http://drive5.com/muscle/' +description = """ MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes—only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s%(version)s_src.tar.gz'] +source_urls = ['http://www.drive5.com/muscle/downloads%(version)s/'] + +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 862ff1060c15af3f1a43b9cb638f217bd06679ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 14:00:19 +0200 Subject: [PATCH 102/722] add easyconfig MUSCLE-3.8.31-foss-2016a.eb --- .../m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb new file mode 100644 index 0000000000..026425a12b --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'http://drive5.com/muscle/' +description = """ MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes—only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s%(version)s_src.tar.gz'] +source_urls = ['http://www.drive5.com/muscle/downloads%(version)s/'] + +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6ad2325b2de444cb179df604acb285eb6c980b12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 14:22:48 +0200 Subject: [PATCH 103/722] add easyconfig R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb --- ...dle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb | 152 ++++++++++++++++++ 1 file changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb new file mode 100644 index 0000000000..d383fdf33e --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb @@ -0,0 +1,152 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', '3.2.3')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.16.1', bioconductor_options), + ('Biobase', '2.30.0', bioconductor_options), + ('S4Vectors', '0.8.11', bioconductor_options), + ('IRanges', '2.4.8', bioconductor_options), + ('GenomeInfoDb', '1.6.3', bioconductor_options), + ('AnnotationDbi', '1.32.3', bioconductor_options), + ('XVector', '0.10.0', bioconductor_options), + ('zlibbioc', '1.16.0', bioconductor_options), + ('Biostrings', '2.38.4', bioconductor_options), + ('GenomicRanges', '1.22.4', bioconductor_options), + ('Rsamtools', '1.22.0', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('BiocParallel', '1.4.3', bioconductor_options), + ('GenomicAlignments', '1.6.3', bioconductor_options), + ('ShortRead', '1.28.0', bioconductor_options), + ('graph', '1.48.0', bioconductor_options), + ('affyio', '1.40.0', bioconductor_options), + ('BiocInstaller', '1.20.1', bioconductor_options), + ('preprocessCore', '1.32.0', bioconductor_options), + ('affy', '1.48.0', bioconductor_options), + ('GO.db', '', bioconductor_options), + ('limma', '3.26.8', bioconductor_options), + ('RBGL', '1.46.0', bioconductor_options), + ('org.Hs.eg.db', '', bioconductor_options), + ('AnnotationForge', '1.12.2', bioconductor_options), + ('KEGG.db', '', bioconductor_options), + ('annaffy', '1.42.0', bioconductor_options), + ('gcrma', '2.42.0', bioconductor_options), + ('oligoClasses', '1.32.0', bioconductor_options), + ('edgeR', '3.12.0', bioconductor_options), + ('PFAM.db', '', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.4.1', bioconductor_options), + ('qvalue', '2.2.2', bioconductor_options), + ('impute', '1.44.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.24.0', bioconductor_options), + ('hgu133plus2.db', '', bioconductor_options), + ('illuminaio', '0.12.0', bioconductor_options), + ('rtracklayer', '1.30.2', bioconductor_options), + ('biomaRt', '2.26.1', bioconductor_options), + ('GenomicFeatures', '1.22.13', bioconductor_options), + ('bumphunter', '1.10.0', bioconductor_options), + ('multtest', '2.26.0', bioconductor_options), + ('siggenes', '1.44.0', bioconductor_options), + ('DynDoc', '1.48.0', bioconductor_options), + ('genoset', '1.24.0', bioconductor_options), + ('NOISeq', '2.14.1', bioconductor_options), + ('Rgraphviz', '2.14.0', bioconductor_options), + ('RNASeqPower', '1.10.0', bioconductor_options), + ('annotate', '1.48.0', bioconductor_options), + ('GSEABase', '1.32.0', bioconductor_options), + ('genefilter', '1.52.1', bioconductor_options), + ('Category', '2.36.0', bioconductor_options), + ('GOstats', '2.36.0', bioconductor_options), + ('BSgenome', '1.38.0', bioconductor_options), + ('VariantAnnotation', '1.16.4', bioconductor_options), + ('biovizBase', '1.18.0', bioconductor_options), + ('OrganismDbi', '1.12.1', bioconductor_options), + ('ggbio', '1.18.5', bioconductor_options), + ('geneplotter', '1.48.0', bioconductor_options), + ('DESeq2', '1.10.1', bioconductor_options), + ('ReportingTools', '2.10.0', bioconductor_options), + ('affycoretools', '1.42.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '', bioconductor_options), + ('Homo.sapiens', '', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '', bioconductor_options), + ('AgiMicroRna', '2.20.0', bioconductor_options), + ('GenomeGraphs', '1.30.0', bioconductor_options), + ('geneLenDataBase', '', bioconductor_options), + ('goseq', '1.22.0', bioconductor_options), + ('KEGGREST', '1.10.1', bioconductor_options), + ('KEGGgraph', '1.28.0', bioconductor_options), + ('KEGGprofile', '1.12.0', bioconductor_options), + ('GEOquery', '2.36.0', bioconductor_options), + ('minfi', '1.16.1', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '', bioconductor_options), + ('methylumi', '2.16.0', bioconductor_options), + ('lumi', '2.22.1', bioconductor_options), + ('widgetTools', '1.48.0', bioconductor_options), + ('tkWidgets', '1.48.0', bioconductor_options), + ('Mfuzz', '2.30.0', bioconductor_options), + ('maSigPro', '1.42.0', bioconductor_options), + ('SPIA', '2.22.0', bioconductor_options), + ('Gviz', '1.14.4', bioconductor_options), + ('cummeRbund', '2.12.1', bioconductor_options), + ('GenomicFiles', '1.6.2', bioconductor_options), + ('derfinderHelper', '1.4.1', bioconductor_options), + ('derfinder', '1.4.4', bioconductor_options), + ('polyester', '1.6.0', bioconductor_options), + ('Rsubread', '1.20.3', bioconductor_options), + ('pcaMethods', '1.60.0', bioconductor_options), + ('marray', '1.48.0', bioconductor_options), + ('CGHbase', '1.30.0', bioconductor_options), + ('sigaR', '1.14.0', bioconductor_options), + ('HCsnip', '1.10.0', bioconductor_options), + ('metagenomeSeq', '1.12.0', bioconductor_options), + ('gdsfmt', '1.6.2', bioconductor_options), + ('SNPRelate', '1.4.2', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From 60ac2c471e4c75e930f78b85fc9315806f75072d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 14:25:56 +0200 Subject: [PATCH 104/722] add easyconfig R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb --- ...dle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 152 ++++++++++++++++++ 1 file changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb new file mode 100644 index 0000000000..43d2df9a2e --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -0,0 +1,152 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', '3.2.3')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.16.1', bioconductor_options), + ('Biobase', '2.30.0', bioconductor_options), + ('S4Vectors', '0.8.11', bioconductor_options), + ('IRanges', '2.4.8', bioconductor_options), + ('GenomeInfoDb', '1.6.3', bioconductor_options), + ('AnnotationDbi', '1.32.3', bioconductor_options), + ('XVector', '0.10.0', bioconductor_options), + ('zlibbioc', '1.16.0', bioconductor_options), + ('Biostrings', '2.38.4', bioconductor_options), + ('GenomicRanges', '1.22.4', bioconductor_options), + ('Rsamtools', '1.22.0', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('BiocParallel', '1.4.3', bioconductor_options), + ('GenomicAlignments', '1.6.3', bioconductor_options), + ('ShortRead', '1.28.0', bioconductor_options), + ('graph', '1.48.0', bioconductor_options), + ('affyio', '1.40.0', bioconductor_options), + ('BiocInstaller', '1.20.1', bioconductor_options), + ('preprocessCore', '1.32.0', bioconductor_options), + ('affy', '1.48.0', bioconductor_options), + ('GO.db', '', bioconductor_options), + ('limma', '3.26.8', bioconductor_options), + ('RBGL', '1.46.0', bioconductor_options), + ('org.Hs.eg.db', '', bioconductor_options), + ('AnnotationForge', '1.12.2', bioconductor_options), + ('KEGG.db', '', bioconductor_options), + ('annaffy', '1.42.0', bioconductor_options), + ('gcrma', '2.42.0', bioconductor_options), + ('oligoClasses', '1.32.0', bioconductor_options), + ('edgeR', '3.12.0', bioconductor_options), + ('PFAM.db', '', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.4.1', bioconductor_options), + ('qvalue', '2.2.2', bioconductor_options), + ('impute', '1.44.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.24.0', bioconductor_options), + ('hgu133plus2.db', '', bioconductor_options), + ('illuminaio', '0.12.0', bioconductor_options), + ('rtracklayer', '1.30.2', bioconductor_options), + ('biomaRt', '2.26.1', bioconductor_options), + ('GenomicFeatures', '1.22.13', bioconductor_options), + ('bumphunter', '1.10.0', bioconductor_options), + ('multtest', '2.26.0', bioconductor_options), + ('siggenes', '1.44.0', bioconductor_options), + ('DynDoc', '1.48.0', bioconductor_options), + ('genoset', '1.24.0', bioconductor_options), + ('NOISeq', '2.14.1', bioconductor_options), + ('Rgraphviz', '2.14.0', bioconductor_options), + ('RNASeqPower', '1.10.0', bioconductor_options), + ('annotate', '1.48.0', bioconductor_options), + ('GSEABase', '1.32.0', bioconductor_options), + ('genefilter', '1.52.1', bioconductor_options), + ('Category', '2.36.0', bioconductor_options), + ('GOstats', '2.36.0', bioconductor_options), + ('BSgenome', '1.38.0', bioconductor_options), + ('VariantAnnotation', '1.16.4', bioconductor_options), + ('biovizBase', '1.18.0', bioconductor_options), + ('OrganismDbi', '1.12.1', bioconductor_options), + ('ggbio', '1.18.5', bioconductor_options), + ('geneplotter', '1.48.0', bioconductor_options), + ('DESeq2', '1.10.1', bioconductor_options), + ('ReportingTools', '2.10.0', bioconductor_options), + ('affycoretools', '1.42.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '', bioconductor_options), + ('Homo.sapiens', '', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '', bioconductor_options), + ('AgiMicroRna', '2.20.0', bioconductor_options), + ('GenomeGraphs', '1.30.0', bioconductor_options), + ('geneLenDataBase', '', bioconductor_options), + ('goseq', '1.22.0', bioconductor_options), + ('KEGGREST', '1.10.1', bioconductor_options), + ('KEGGgraph', '1.28.0', bioconductor_options), + ('KEGGprofile', '1.12.0', bioconductor_options), + ('GEOquery', '2.36.0', bioconductor_options), + ('minfi', '1.16.1', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '', bioconductor_options), + ('methylumi', '2.16.0', bioconductor_options), + ('lumi', '2.22.1', bioconductor_options), + ('widgetTools', '1.48.0', bioconductor_options), + ('tkWidgets', '1.48.0', bioconductor_options), + ('Mfuzz', '2.30.0', bioconductor_options), + ('maSigPro', '1.42.0', bioconductor_options), + ('SPIA', '2.22.0', bioconductor_options), + ('Gviz', '1.14.4', bioconductor_options), + ('cummeRbund', '2.12.1', bioconductor_options), + ('GenomicFiles', '1.6.2', bioconductor_options), + ('derfinderHelper', '1.4.1', bioconductor_options), + ('derfinder', '1.4.4', bioconductor_options), + ('polyester', '1.6.0', bioconductor_options), + ('Rsubread', '1.20.3', bioconductor_options), + ('pcaMethods', '1.60.0', bioconductor_options), + ('marray', '1.48.0', bioconductor_options), + ('CGHbase', '1.30.0', bioconductor_options), + ('sigaR', '1.14.0', bioconductor_options), + ('HCsnip', '1.10.0', bioconductor_options), + ('metagenomeSeq', '1.12.0', bioconductor_options), + ('gdsfmt', '1.6.2', bioconductor_options), + ('SNPRelate', '1.4.2', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From b66998ce4164d27da3f9e01567ec7e5dabffb228 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 14:40:58 +0200 Subject: [PATCH 105/722] modify easyconfig R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb --- ...dle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 43d2df9a2e..47a6df9dac 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -29,9 +29,9 @@ bioconductor_options = { 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', ], 'source_tmpl': name_tmpl, } @@ -61,24 +61,24 @@ exts_list = [ ('BiocInstaller', '1.20.1', bioconductor_options), ('preprocessCore', '1.32.0', bioconductor_options), ('affy', '1.48.0', bioconductor_options), - ('GO.db', '', bioconductor_options), + ('GO.db', '3.2.2', bioconductor_options), ('limma', '3.26.8', bioconductor_options), ('RBGL', '1.46.0', bioconductor_options), - ('org.Hs.eg.db', '', bioconductor_options), + ('org.Hs.eg.db', '3.2.3', bioconductor_options), ('AnnotationForge', '1.12.2', bioconductor_options), - ('KEGG.db', '', bioconductor_options), + ('KEGG.db', '3.2.2', bioconductor_options), ('annaffy', '1.42.0', bioconductor_options), ('gcrma', '2.42.0', bioconductor_options), ('oligoClasses', '1.32.0', bioconductor_options), ('edgeR', '3.12.0', bioconductor_options), - ('PFAM.db', '', bioconductor_options), + ('PFAM.db', '3.2.2', bioconductor_options), ('perm', '1.0-0.0', ext_options), ('baySeq', '2.4.1', bioconductor_options), ('qvalue', '2.2.2', bioconductor_options), ('impute', '1.44.0', bioconductor_options), ('samr', '2.0', ext_options), ('DEGseq', '1.24.0', bioconductor_options), - ('hgu133plus2.db', '', bioconductor_options), + ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), ('rtracklayer', '1.30.2', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), @@ -105,19 +105,19 @@ exts_list = [ ('DESeq2', '1.10.1', bioconductor_options), ('ReportingTools', '2.10.0', bioconductor_options), ('affycoretools', '1.42.0', bioconductor_options), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '', bioconductor_options), - ('Homo.sapiens', '', bioconductor_options), - ('BSgenome.Hsapiens.UCSC.hg19', '', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', bioconductor_options), + ('Homo.sapiens', '1.3.1', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), ('AgiMicroRna', '2.20.0', bioconductor_options), ('GenomeGraphs', '1.30.0', bioconductor_options), - ('geneLenDataBase', '', bioconductor_options), + ('geneLenDataBase', '1.6.0', bioconductor_options), ('goseq', '1.22.0', bioconductor_options), ('KEGGREST', '1.10.1', bioconductor_options), ('KEGGgraph', '1.28.0', bioconductor_options), ('KEGGprofile', '1.12.0', bioconductor_options), ('GEOquery', '2.36.0', bioconductor_options), ('minfi', '1.16.1', bioconductor_options), - ('FDb.InfiniumMethylation.hg19', '', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), ('methylumi', '2.16.0', bioconductor_options), ('lumi', '2.22.1', bioconductor_options), ('widgetTools', '1.48.0', bioconductor_options), -- GitLab From 3240a23cad4ea79d6fcc1695fb8db8f4489a07ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 13:48:50 +0100 Subject: [PATCH 106/722] add phangorn extension in R 3.2.3 easyconfigs --- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 1 + easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb | 1 + easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 1 + easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index dcabcfedb0..966d48e3c9 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -438,6 +438,7 @@ exts_list = [ ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.2', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb index bc318c4a60..323a1f2507 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -438,6 +438,7 @@ exts_list = [ ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.2', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index 49fadf4c1f..2fead5c720 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -450,6 +450,7 @@ exts_list = [ ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.2', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index ddf0479c12..91dc12b964 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -438,6 +438,7 @@ exts_list = [ ('qgraph', '1.3.2', ext_options), ('diveRsity', '1.9.89', ext_options), ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.2', ext_options), ] moduleclass = 'lang' -- GitLab From 18427a87b82e5d144a995851376c100da8b2389f Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 10 Mar 2016 15:22:31 +0100 Subject: [PATCH 107/722] Fix OS dependencies for MVAPICH2 with BLCR checkpoint/restart support --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index cee59253ac..6cd874bb9a 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -23,7 +23,10 @@ dependencies = [('hwloc', '1.5.1')] # enable checkpointing support withchkpt = True -osdependencies = ['blcr-libs', 'blcr-devel'] +osdependencies = [ + ('libcr-dev', 'blcr-devel'), + ('libattr1-dev', 'libattr-devel'), +] builddependencies = [('Bison', '2.5')] -- GitLab From cd6eed7dbf4cde9809f8c0dadfa96317fc62934c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 17:01:20 +0200 Subject: [PATCH 108/722] modify easyconfig R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb, add easyconfig R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb --- ...dle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 6 +- ...le-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 154 ++++++++++++++++++ 2 files changed, 158 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 47a6df9dac..747435a5bf 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -45,15 +45,16 @@ exts_list = [ ('IRanges', '2.4.8', bioconductor_options), ('GenomeInfoDb', '1.6.3', bioconductor_options), ('AnnotationDbi', '1.32.3', bioconductor_options), - ('XVector', '0.10.0', bioconductor_options), ('zlibbioc', '1.16.0', bioconductor_options), + ('XVector', '0.10.0', bioconductor_options), ('Biostrings', '2.38.4', bioconductor_options), ('GenomicRanges', '1.22.4', bioconductor_options), + ('BiocParallel', '1.4.3', bioconductor_options), ('Rsamtools', '1.22.0', bioconductor_options), ('lambda.r', '1.1.7', ext_options), ('futile.options', '1.0.0', ext_options), ('futile.logger', '1.4.1', ext_options), - ('BiocParallel', '1.4.3', bioconductor_options), + ('SummarizedExperiment', '1.0.2', bioconductor_options), ('GenomicAlignments', '1.6.3', bioconductor_options), ('ShortRead', '1.28.0', bioconductor_options), ('graph', '1.48.0', bioconductor_options), @@ -116,6 +117,7 @@ exts_list = [ ('KEGGgraph', '1.28.0', bioconductor_options), ('KEGGprofile', '1.12.0', bioconductor_options), ('GEOquery', '2.36.0', bioconductor_options), + ('mixOmics', '5.2.0', ext_options), ('minfi', '1.16.1', bioconductor_options), ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), ('methylumi', '2.16.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb new file mode 100644 index 0000000000..f4c9219e9d --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -0,0 +1,154 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', '3.2.3')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.16.1', bioconductor_options), + ('Biobase', '2.30.0', bioconductor_options), + ('S4Vectors', '0.8.11', bioconductor_options), + ('IRanges', '2.4.8', bioconductor_options), + ('GenomeInfoDb', '1.6.3', bioconductor_options), + ('AnnotationDbi', '1.32.3', bioconductor_options), + ('zlibbioc', '1.16.0', bioconductor_options), + ('XVector', '0.10.0', bioconductor_options), + ('Biostrings', '2.38.4', bioconductor_options), + ('GenomicRanges', '1.22.4', bioconductor_options), + ('BiocParallel', '1.4.3', bioconductor_options), + ('Rsamtools', '1.22.0', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('SummarizedExperiment', '1.0.2', bioconductor_options), + ('GenomicAlignments', '1.6.3', bioconductor_options), + ('ShortRead', '1.28.0', bioconductor_options), + ('graph', '1.48.0', bioconductor_options), + ('affyio', '1.40.0', bioconductor_options), + ('BiocInstaller', '1.20.1', bioconductor_options), + ('preprocessCore', '1.32.0', bioconductor_options), + ('affy', '1.48.0', bioconductor_options), + ('GO.db', '3.2.2', bioconductor_options), + ('limma', '3.26.8', bioconductor_options), + ('RBGL', '1.46.0', bioconductor_options), + ('org.Hs.eg.db', '3.2.3', bioconductor_options), + ('AnnotationForge', '1.12.2', bioconductor_options), + ('KEGG.db', '3.2.2', bioconductor_options), + ('annaffy', '1.42.0', bioconductor_options), + ('gcrma', '2.42.0', bioconductor_options), + ('oligoClasses', '1.32.0', bioconductor_options), + ('edgeR', '3.12.0', bioconductor_options), + ('PFAM.db', '3.2.2', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.4.1', bioconductor_options), + ('qvalue', '2.2.2', bioconductor_options), + ('impute', '1.44.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.24.0', bioconductor_options), + ('hgu133plus2.db', '3.2.2', bioconductor_options), + ('illuminaio', '0.12.0', bioconductor_options), + ('rtracklayer', '1.30.2', bioconductor_options), + ('biomaRt', '2.26.1', bioconductor_options), + ('GenomicFeatures', '1.22.13', bioconductor_options), + ('bumphunter', '1.10.0', bioconductor_options), + ('multtest', '2.26.0', bioconductor_options), + ('siggenes', '1.44.0', bioconductor_options), + ('DynDoc', '1.48.0', bioconductor_options), + ('genoset', '1.24.0', bioconductor_options), + ('NOISeq', '2.14.1', bioconductor_options), + ('Rgraphviz', '2.14.0', bioconductor_options), + ('RNASeqPower', '1.10.0', bioconductor_options), + ('annotate', '1.48.0', bioconductor_options), + ('GSEABase', '1.32.0', bioconductor_options), + ('genefilter', '1.52.1', bioconductor_options), + ('Category', '2.36.0', bioconductor_options), + ('GOstats', '2.36.0', bioconductor_options), + ('BSgenome', '1.38.0', bioconductor_options), + ('VariantAnnotation', '1.16.4', bioconductor_options), + ('biovizBase', '1.18.0', bioconductor_options), + ('OrganismDbi', '1.12.1', bioconductor_options), + ('ggbio', '1.18.5', bioconductor_options), + ('geneplotter', '1.48.0', bioconductor_options), + ('DESeq2', '1.10.1', bioconductor_options), + ('ReportingTools', '2.10.0', bioconductor_options), + ('affycoretools', '1.42.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', bioconductor_options), + ('Homo.sapiens', '1.3.1', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.20.0', bioconductor_options), + ('GenomeGraphs', '1.30.0', bioconductor_options), + ('geneLenDataBase', '1.6.0', bioconductor_options), + ('goseq', '1.22.0', bioconductor_options), + ('KEGGREST', '1.10.1', bioconductor_options), + ('KEGGgraph', '1.28.0', bioconductor_options), + ('KEGGprofile', '1.12.0', bioconductor_options), + ('GEOquery', '2.36.0', bioconductor_options), + ('mixOmics', '5.2.0', ext_options), + ('minfi', '1.16.1', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.16.0', bioconductor_options), + ('lumi', '2.22.1', bioconductor_options), + ('widgetTools', '1.48.0', bioconductor_options), + ('tkWidgets', '1.48.0', bioconductor_options), + ('Mfuzz', '2.30.0', bioconductor_options), + ('maSigPro', '1.42.0', bioconductor_options), + ('SPIA', '2.22.0', bioconductor_options), + ('Gviz', '1.14.4', bioconductor_options), + ('cummeRbund', '2.12.1', bioconductor_options), + ('GenomicFiles', '1.6.2', bioconductor_options), + ('derfinderHelper', '1.4.1', bioconductor_options), + ('derfinder', '1.4.4', bioconductor_options), + ('polyester', '1.6.0', bioconductor_options), + ('Rsubread', '1.20.3', bioconductor_options), + ('pcaMethods', '1.60.0', bioconductor_options), + ('marray', '1.48.0', bioconductor_options), + ('CGHbase', '1.30.0', bioconductor_options), + ('sigaR', '1.14.0', bioconductor_options), + ('HCsnip', '1.10.0', bioconductor_options), + ('metagenomeSeq', '1.12.0', bioconductor_options), + ('gdsfmt', '1.6.2', bioconductor_options), + ('SNPRelate', '1.4.2', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From baf9329fdbc191d90ae2a5f392a6ef9b6c12df9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Mar 2016 16:52:26 +0100 Subject: [PATCH 109/722] remove wrong easyconfig --- ...dle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb | 152 ------------------ 1 file changed, 152 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb deleted file mode 100644 index d383fdf33e..0000000000 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-foss-2016a-R-3.2.3.eb +++ /dev/null @@ -1,152 +0,0 @@ -easyblock = 'Bundle' - -name = 'R-bundle-Bioconductor' -version = '3.1' -versionsuffix = '-R-%(rver)s' - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -# these are extensions for R -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -dependencies = [('R', '3.2.3')] - -name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib/', # current version of packages - 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': name_tmpl, -} -bioconductor_options = { - 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', - ], - 'source_tmpl': name_tmpl, -} - -# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends -# !! order of packages is important !! -exts_list = [ - ('BiocGenerics', '0.16.1', bioconductor_options), - ('Biobase', '2.30.0', bioconductor_options), - ('S4Vectors', '0.8.11', bioconductor_options), - ('IRanges', '2.4.8', bioconductor_options), - ('GenomeInfoDb', '1.6.3', bioconductor_options), - ('AnnotationDbi', '1.32.3', bioconductor_options), - ('XVector', '0.10.0', bioconductor_options), - ('zlibbioc', '1.16.0', bioconductor_options), - ('Biostrings', '2.38.4', bioconductor_options), - ('GenomicRanges', '1.22.4', bioconductor_options), - ('Rsamtools', '1.22.0', bioconductor_options), - ('lambda.r', '1.1.7', ext_options), - ('futile.options', '1.0.0', ext_options), - ('futile.logger', '1.4.1', ext_options), - ('BiocParallel', '1.4.3', bioconductor_options), - ('GenomicAlignments', '1.6.3', bioconductor_options), - ('ShortRead', '1.28.0', bioconductor_options), - ('graph', '1.48.0', bioconductor_options), - ('affyio', '1.40.0', bioconductor_options), - ('BiocInstaller', '1.20.1', bioconductor_options), - ('preprocessCore', '1.32.0', bioconductor_options), - ('affy', '1.48.0', bioconductor_options), - ('GO.db', '', bioconductor_options), - ('limma', '3.26.8', bioconductor_options), - ('RBGL', '1.46.0', bioconductor_options), - ('org.Hs.eg.db', '', bioconductor_options), - ('AnnotationForge', '1.12.2', bioconductor_options), - ('KEGG.db', '', bioconductor_options), - ('annaffy', '1.42.0', bioconductor_options), - ('gcrma', '2.42.0', bioconductor_options), - ('oligoClasses', '1.32.0', bioconductor_options), - ('edgeR', '3.12.0', bioconductor_options), - ('PFAM.db', '', bioconductor_options), - ('perm', '1.0-0.0', ext_options), - ('baySeq', '2.4.1', bioconductor_options), - ('qvalue', '2.2.2', bioconductor_options), - ('impute', '1.44.0', bioconductor_options), - ('samr', '2.0', ext_options), - ('DEGseq', '1.24.0', bioconductor_options), - ('hgu133plus2.db', '', bioconductor_options), - ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.2', bioconductor_options), - ('biomaRt', '2.26.1', bioconductor_options), - ('GenomicFeatures', '1.22.13', bioconductor_options), - ('bumphunter', '1.10.0', bioconductor_options), - ('multtest', '2.26.0', bioconductor_options), - ('siggenes', '1.44.0', bioconductor_options), - ('DynDoc', '1.48.0', bioconductor_options), - ('genoset', '1.24.0', bioconductor_options), - ('NOISeq', '2.14.1', bioconductor_options), - ('Rgraphviz', '2.14.0', bioconductor_options), - ('RNASeqPower', '1.10.0', bioconductor_options), - ('annotate', '1.48.0', bioconductor_options), - ('GSEABase', '1.32.0', bioconductor_options), - ('genefilter', '1.52.1', bioconductor_options), - ('Category', '2.36.0', bioconductor_options), - ('GOstats', '2.36.0', bioconductor_options), - ('BSgenome', '1.38.0', bioconductor_options), - ('VariantAnnotation', '1.16.4', bioconductor_options), - ('biovizBase', '1.18.0', bioconductor_options), - ('OrganismDbi', '1.12.1', bioconductor_options), - ('ggbio', '1.18.5', bioconductor_options), - ('geneplotter', '1.48.0', bioconductor_options), - ('DESeq2', '1.10.1', bioconductor_options), - ('ReportingTools', '2.10.0', bioconductor_options), - ('affycoretools', '1.42.0', bioconductor_options), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '', bioconductor_options), - ('Homo.sapiens', '', bioconductor_options), - ('BSgenome.Hsapiens.UCSC.hg19', '', bioconductor_options), - ('AgiMicroRna', '2.20.0', bioconductor_options), - ('GenomeGraphs', '1.30.0', bioconductor_options), - ('geneLenDataBase', '', bioconductor_options), - ('goseq', '1.22.0', bioconductor_options), - ('KEGGREST', '1.10.1', bioconductor_options), - ('KEGGgraph', '1.28.0', bioconductor_options), - ('KEGGprofile', '1.12.0', bioconductor_options), - ('GEOquery', '2.36.0', bioconductor_options), - ('minfi', '1.16.1', bioconductor_options), - ('FDb.InfiniumMethylation.hg19', '', bioconductor_options), - ('methylumi', '2.16.0', bioconductor_options), - ('lumi', '2.22.1', bioconductor_options), - ('widgetTools', '1.48.0', bioconductor_options), - ('tkWidgets', '1.48.0', bioconductor_options), - ('Mfuzz', '2.30.0', bioconductor_options), - ('maSigPro', '1.42.0', bioconductor_options), - ('SPIA', '2.22.0', bioconductor_options), - ('Gviz', '1.14.4', bioconductor_options), - ('cummeRbund', '2.12.1', bioconductor_options), - ('GenomicFiles', '1.6.2', bioconductor_options), - ('derfinderHelper', '1.4.1', bioconductor_options), - ('derfinder', '1.4.4', bioconductor_options), - ('polyester', '1.6.0', bioconductor_options), - ('Rsubread', '1.20.3', bioconductor_options), - ('pcaMethods', '1.60.0', bioconductor_options), - ('marray', '1.48.0', bioconductor_options), - ('CGHbase', '1.30.0', bioconductor_options), - ('sigaR', '1.14.0', bioconductor_options), - ('HCsnip', '1.10.0', bioconductor_options), - ('metagenomeSeq', '1.12.0', bioconductor_options), - ('gdsfmt', '1.6.2', bioconductor_options), - ('SNPRelate', '1.4.2', bioconductor_options), -] - -modextrapaths = {'R_LIBS': ''} - -sanity_check_paths = { - 'files': [], - 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], -} - -moduleclass = 'bio' -- GitLab From 3b61720f9d6aba21e540624b2805dff29f21ad84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 10:44:27 +0100 Subject: [PATCH 110/722] drop 'release' URLs, don't use %(rver)s yet --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 7 +++---- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 8 +++----- 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 747435a5bf..d5dcde11e2 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -13,7 +13,9 @@ toolchain = {'name': 'foss', 'version': '2016a'} exts_defaultclass = 'RPackage' exts_filter = ("R -q --no-save", "library(%(ext_name)s)") -dependencies = [('R', '3.2.3')] +rver = '3.2.3' +versionsuffix = '-R-%s' % rver +dependencies = [('R', rver)] name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { @@ -26,9 +28,6 @@ ext_options = { } bioconductor_options = { 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index f4c9219e9d..dce3357e77 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -2,7 +2,6 @@ easyblock = 'Bundle' name = 'R-bundle-Bioconductor' version = '3.2' -versionsuffix = '-R-%(rver)s' homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -13,7 +12,9 @@ toolchain = {'name': 'intel', 'version': '2016a'} exts_defaultclass = 'RPackage' exts_filter = ("R -q --no-save", "library(%(ext_name)s)") -dependencies = [('R', '3.2.3')] +rver = '3.2.3' +versionsuffix = '-R-%s' % rver +dependencies = [('R', rver)] name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { @@ -26,9 +27,6 @@ ext_options = { } bioconductor_options = { 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', -- GitLab From 782e024dbab561cbe68d02bfd5d917f995130911 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 11 Mar 2016 12:28:22 +0200 Subject: [PATCH 111/722] add easyconfig GDB-7.11-intel-2016a.eb --- .../easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb new file mode 100644 index 0000000000..fa5295e98e --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.11' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('expat', '2.1.0'), + ('Python', '2.7.11'), +] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' -- GitLab From 90276c29d80a68782f1eb9b092ac8265f4c2baf1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 13:04:48 +0200 Subject: [PATCH 112/722] add easyconfig PHYLIP-3.696-intel-2016a.eb --- .../p/PHYLIP/PHYLIP-3.696-intel-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb new file mode 100644 index 0000000000..337f4f3b90 --- /dev/null +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'PHYLIP' +version = '3.696' + +homepage = 'http://evolution.genetics.washington.edu/phylip' +description = "PHYLIP is a free package of programs for inferring phylogenies." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://evolution.gs.washington.edu/phylip/download/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' + +files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.so', 'src/libdrawtree.so'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' -- GitLab From 0b7c8c0733734518db9d852ba8a112126cbe20bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 13:06:50 +0200 Subject: [PATCH 113/722] add easyconfig BWA-0.7.13-intel-2016a.eb --- .../b/BWA/BWA-0.7.13-intel-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb new file mode 100644 index 0000000000..f4774cbbbe --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.13 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.13' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +moduleclass = 'bio' -- GitLab From d264046fac6218f20a0610d5c0b069e3a1324253 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 13:17:08 +0200 Subject: [PATCH 114/722] add easyconfig SNPhylo-20140701-intel-2016a.eb, add easyconfig SNPhylo-20140701-foss-2016a.eb --- .../s/SNPhylo/SNPhylo-20140701-foss-2016a.eb | 22 +++++++++++++++++++ .../s/SNPhylo/SNPhylo-20140701-intel-2016a.eb | 22 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb new file mode 100644 index 0000000000..e61334d314 --- /dev/null +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'SNPhylo' +version = '20140701' + +homepage = 'http://chibba.pgml.uga.edu/snphylo/' +description = """SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# download from http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz and rename +# see http://chibba.pgml.uga.edu/snphylo/ for version +sources = ['%(namelower)s-%(version)s.tar.gz'] + +checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] + +dependencies = [ + ('R', '3.2.3'), + ('Python', '2.7.11'), + ('MUSCLE', '3.8.31'), + ('PHYLIP', '3.696'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb new file mode 100644 index 0000000000..cea99bc814 --- /dev/null +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'SNPhylo' +version = '20140701' + +homepage = 'http://chibba.pgml.uga.edu/snphylo/' +description = """SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# download from http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz and rename +# see http://chibba.pgml.uga.edu/snphylo/ for version +sources = ['%(namelower)s-%(version)s.tar.gz'] + +checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] + +dependencies = [ + ('R', '3.2.3'), + ('Python', '2.7.11'), + ('MUSCLE', '3.8.31'), + ('PHYLIP', '3.696'), +] + +moduleclass = 'bio' -- GitLab From 5649cc342580e1a881db0e6a949b4a118bf45f9b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 14:47:59 +0200 Subject: [PATCH 115/722] add easyconfig npstat-0.99-intel-2016a.eb --- .../n/npstat/npstat-0.99-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/npstat/npstat-0.99-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/npstat/npstat-0.99-intel-2016a.eb b/easybuild/easyconfigs/n/npstat/npstat-0.99-intel-2016a.eb new file mode 100644 index 0000000000..b8f9940b59 --- /dev/null +++ b/easybuild/easyconfigs/n/npstat/npstat-0.99-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'npstat' +version = '0.99' + +homepage = 'https://code.google.com/archive/p/npstat/' +description = """npstat implements some population genetics tests and estimators that can be applied + to pooled sequences from Next Generation Sequencing experiments.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://storage.googleapis.com/google-code-archive-source/v2/code.google.com/npstat/'] +sources = ['source-archive.zip'] + +patches = ['npstat-%(version)s_fix-hardcoding-Makefile.patch'] + +# commit 14, Oct 31st 2013 +checksums = ['a1595b7c46312d0f51b8b68987289337'] + +dependencies = [ + ('GSL', '1.16'), +] + +start_dir = 'trunk' + +files_to_copy = [(['npstat'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/npstat'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 69480c1a1e0803e198c1d9a449bcb849fde15c03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 14:53:38 +0200 Subject: [PATCH 116/722] modify easyconfig SNPhylo-20140701-intel-2016a.eb, modify easyconfig SNPhylo-20140701-foss-2016a.eb --- easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb | 1 + easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb index e61334d314..6fb5d3516e 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb @@ -14,6 +14,7 @@ checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] dependencies = [ ('R', '3.2.3'), + ('R-bundle-Bioconductor', '3.2', 'R-%(rver)s'), ('Python', '2.7.11'), ('MUSCLE', '3.8.31'), ('PHYLIP', '3.696'), diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb index cea99bc814..45955d802a 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb @@ -14,6 +14,7 @@ checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] dependencies = [ ('R', '3.2.3'), + ('R-bundle-Bioconductor', '3.2', 'R-%(rver)s'), ('Python', '2.7.11'), ('MUSCLE', '3.8.31'), ('PHYLIP', '3.696'), -- GitLab From 1cc3e64db7e1faa91730799ae3c9c25281139c4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 14:55:28 +0200 Subject: [PATCH 117/722] modify easyconfig SNPhylo-20140701-intel-2016a.eb, modify easyconfig SNPhylo-20140701-foss-2016a.eb --- easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb | 2 +- easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb index 6fb5d3516e..701dafb78c 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb @@ -14,7 +14,7 @@ checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] dependencies = [ ('R', '3.2.3'), - ('R-bundle-Bioconductor', '3.2', 'R-%(rver)s'), + ('R-bundle-Bioconductor', '3.2', '-R-%(rver)s'), ('Python', '2.7.11'), ('MUSCLE', '3.8.31'), ('PHYLIP', '3.696'), diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb index 45955d802a..71e1b6e3e1 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb @@ -14,7 +14,7 @@ checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] dependencies = [ ('R', '3.2.3'), - ('R-bundle-Bioconductor', '3.2', 'R-%(rver)s'), + ('R-bundle-Bioconductor', '3.2', '-R-%(rver)s'), ('Python', '2.7.11'), ('MUSCLE', '3.8.31'), ('PHYLIP', '3.696'), -- GitLab From 9538cef30f7081f37b819bb5edf8b5542f397432 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 14:02:37 +0100 Subject: [PATCH 118/722] fix remark --- easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb index 090561e4d6..90aea78df7 100644 --- a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb @@ -9,7 +9,7 @@ description = "PHYLIP is a free package of programs for inferring phylogenies." toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://evolution.gs.washington.edu/phylip/download/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb index 337f4f3b90..312062d04f 100644 --- a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb @@ -9,7 +9,7 @@ description = "PHYLIP is a free package of programs for inferring phylogenies." toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://evolution.gs.washington.edu/phylip/download/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' -- GitLab From 10e9af18743b647aedec72e30e300e9d8cf249f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 15:15:16 +0200 Subject: [PATCH 119/722] modify easyconfig SNPhylo-20140701-intel-2016a.eb, modify easyconfig SNPhylo-20140701-foss-2016a.eb --- easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb | 2 +- easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb index 701dafb78c..f27160e9e4 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-foss-2016a.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} # download from http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz and rename # see http://chibba.pgml.uga.edu/snphylo/ for version -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb index 71e1b6e3e1..d54fcc2b47 100644 --- a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20140701-intel-2016a.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # download from http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz and rename # see http://chibba.pgml.uga.edu/snphylo/ for version -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['80f31c46f1fa9c0c459f18d3acf9fa25'] -- GitLab From 994c84656ccbe2f1b81547066f44e9cf6d531008 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 14:49:25 +0100 Subject: [PATCH 120/722] add missing dependencines in Python 3.5.x easyconfigs --- easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index ae86e7bce7..6b562baa0c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -19,6 +19,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index 38309ea23d..ec80435d9b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -19,6 +19,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index e610aff618..aa7a7d9034 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -19,6 +19,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -- GitLab From dc3792dcd107de914d6f2c690f76e425570727bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 17:22:01 +0200 Subject: [PATCH 121/722] add easyconfig attr-2.4.47-GCC-4.6.3.eb --- .../a/attr/attr-2.4.47-GCC-4.6.3.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb diff --git a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb new file mode 100644 index 0000000000..7d040cf36d --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.4.47' + +homepage = 'http://savannah.nongnu.org/projects/attr' +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCC', 'version': '4.6.3'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = ['attr-%(version)s.src.tar.gz'] + +installopts = 'install-lib' + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'lib/libattr.so.1', 'lib/libattr.so.1.1.0'], + 'dirs': ['share'], +} + +moduleclass = 'tools' -- GitLab From de64fa3397823e88d287c726e03037d5950b5733 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 16:36:40 +0100 Subject: [PATCH 122/722] add 'attr' as dep in MVAPICH2 easyconfig w/ checkpointing support enabled --- .../MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 6cd874bb9a..04c6dccfe0 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -11,24 +11,26 @@ toolchain = {'name': 'GCC', 'version': '4.6.3'} sources = [SOURCELOWER_TGZ] # note: this URL will only work for the most recent version (previous versions no longer available?) source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] +dependencies = [ + ('hwloc', '1.5.1'), + ('attr', '2.4.47'), +] + +builddependencies = [('Bison', '2.5')] + +osdependencies = [('libcr-dev', 'blcr-devel'),] -rdma_type = "gen2" # 'gen2' or 'udapl' +# 'gen2' or 'udapl' +rdma_type = 'gen2' # enable building of MPE routines withmpe = True # enable hwloc support withhwloc = True -dependencies = [('hwloc', '1.5.1')] # enable checkpointing support withchkpt = True -osdependencies = [ - ('libcr-dev', 'blcr-devel'), - ('libattr1-dev', 'libattr-devel'), -] - -builddependencies = [('Bison', '2.5')] # parallel build tends to fail parallel = 1 -- GitLab From 0ca0ceb1e538326be9741280b130b54e399a4a77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 18:09:52 +0200 Subject: [PATCH 123/722] modify easyconfig attr-2.4.47-GCC-4.6.3.eb --- easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb index 7d040cf36d..5c73e6a27b 100644 --- a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb @@ -11,11 +11,11 @@ toolchain = {'name': 'GCC', 'version': '4.6.3'} source_urls = [GNU_SAVANNAH_SOURCE] sources = ['attr-%(version)s.src.tar.gz'] -installopts = 'install-lib' +installopts = 'install-dev install-lib' sanity_check_paths = { 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'lib/libattr.so.1', 'lib/libattr.so.1.1.0'], - 'dirs': ['share'], + 'dirs': ['include/attr', 'share'], } moduleclass = 'tools' -- GitLab From a3451e115fa85fef0f3ccaeeb6bec8be8a6070ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 18:22:53 +0200 Subject: [PATCH 124/722] modify easyconfig attr-2.4.47-GCC-4.6.3.eb --- easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb index 5c73e6a27b..3f29b7d6d3 100644 --- a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb @@ -14,7 +14,7 @@ sources = ['attr-%(version)s.src.tar.gz'] installopts = 'install-dev install-lib' sanity_check_paths = { - 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'lib/libattr.so.1', 'lib/libattr.so.1.1.0'], + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'lib/libattr.a', 'lib/libattr.%s' % SHLIB_EXT], 'dirs': ['include/attr', 'share'], } -- GitLab From d51a1b8e4a249e60c7872f858a1207e59138e134 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 18:58:56 +0200 Subject: [PATCH 125/722] modify easyconfig attr-2.4.47-GCC-4.6.3.eb --- easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb index 3f29b7d6d3..8a4e822bba 100644 --- a/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/a/attr/attr-2.4.47-GCC-4.6.3.eb @@ -14,8 +14,9 @@ sources = ['attr-%(version)s.src.tar.gz'] installopts = 'install-dev install-lib' sanity_check_paths = { - 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'lib/libattr.a', 'lib/libattr.%s' % SHLIB_EXT], - 'dirs': ['include/attr', 'share'], + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', 'include/attr/attributes.h', 'include/attr/error_context.h', + 'include/attr/libattr.h', 'include/attr/xattr.h', 'lib/libattr.a', 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], } moduleclass = 'tools' -- GitLab From 4754be502808e9896a96f2dc2acd816aa62e40ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 18:46:05 +0100 Subject: [PATCH 126/722] consistently add checksums --- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 3 +++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb | 2 ++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb | 1 - .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb | 1 - .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb | 1 - easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb | 1 - .../m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb | 1 - easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb | 2 ++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb | 2 ++ .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb | 2 ++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb | 2 ++ easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb | 1 - 12 files changed, 13 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index a2fae1e4c8..0d8dbcbf47 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -11,6 +11,9 @@ toolchain = {'name': 'GCC', 'version': '4.6.3'} sources = [SOURCELOWER_TGZ] # note: this URL will only work for the most recent version (previous versions no longer available?) source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] + +checksums = ['b05c3cde3d181b2499500b4bd8962e3f'] + dependencies = [ ('hwloc', '1.5.1'), ('attr', '2.4.47'), diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb index 76de06e6fd..8f93aad7e1 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb @@ -11,6 +11,8 @@ sources = [SOURCELOWER_TGZ] # note: this URL will only work for the most recent version (previous versions no longer available?) source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] +checksums = ['b05c3cde3d181b2499500b4bd8962e3f'] + builddependencies = [('Bison', '2.5')] # enable building of MPE routines diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb index dbf130a107..f289c8d654 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['ef4ae05e3b5ad485326505db7381246c'] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb index f8ed601fa4..09e0392913 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['5dc58ed08fd3142c260b70fe297e127c'] dependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb index ec3097f101..8c81cfba65 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'ClangGCC', 'version': '1.2.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['5dc58ed08fd3142c260b70fe297e127c'] dependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb index fc82223d21..87eee23607 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['5dc58ed08fd3142c260b70fe297e127c'] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb index 2ff528acce..5bcb7de6da 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb @@ -10,7 +10,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['5dc58ed08fd3142c260b70fe297e127c'] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb index 86fdc73adc..372dd0b722 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb @@ -9,6 +9,8 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +checksums = ['9d517d6fe483ad339ea01fa234f0c4c9'] + builddependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb index 1c45f04807..657cf1ea16 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb @@ -9,6 +9,8 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +checksums = ['dfc86a014666776c8a76bb8e78356c8b'] + builddependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb index 892dac4687..efbb18826b 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb @@ -9,6 +9,8 @@ toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +checksums = ['0a236f526e368e12a1b3de90716a12d7'] + builddependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb index 9e7d8d7641..46ea0c6676 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb @@ -9,6 +9,8 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] +checksums = ['0a236f526e368e12a1b3de90716a12d7'] + builddependencies = [('Bison', '2.7')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb index bf2762a1a1..b07b0a30f4 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/'] sources = [SOURCELOWER_TAR_GZ] -# Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['77bba29442f81e196155e87869cdceda'] builddependencies = [('Bison', '2.7')] -- GitLab From 5def8be0d16d4175188ecd8eb939b2ba7bb14829 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 20:01:23 +0200 Subject: [PATCH 127/722] add easyconfig SAMtools-1.3-foss-2016a.eb, add easyconfig SAMtools-1.3-intel-2016a.eb --- .../s/SAMtools/SAMtools-1.3-foss-2016a.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3-intel-2016a.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb new file mode 100644 index 0000000000..96d3b95f0f --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb new file mode 100644 index 0000000000..d869d21007 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' -- GitLab From 2067db8a1de479e20c7faee94ee6e93ec9704021 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 20:02:26 +0200 Subject: [PATCH 128/722] add easyconfig VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb, add easyconfig VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb --- .../VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb | 37 +++++++++++++++++++ ...VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..c7db740277 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.14' +versionsuffix = '-Perl-%(perlver)s' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.22.1'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..9f1d001bfa --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.14' +versionsuffix = '-Perl-%(perlver)s' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.22.1'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 84ad66c690b657863777d5b1f16621ffc995a0d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 19:05:58 +0100 Subject: [PATCH 129/722] fix source URLs for Bioconductor 3.2 --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 6 +++--- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index d5dcde11e2..d1392d23cc 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -28,9 +28,9 @@ ext_options = { } bioconductor_options = { 'source_urls': [ - 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/data/experiment/src/contrib/', ], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index dce3357e77..60d39797ec 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -27,9 +27,9 @@ ext_options = { } bioconductor_options = { 'source_urls': [ - 'http://www.bioconductor.org/packages/%(version)s/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/%(version)s/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/%(version)s/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.2/data/experiment/src/contrib/', ], 'source_tmpl': name_tmpl, } -- GitLab From 4606a7f6ce37e1ca5222629d13d1842c4ede1411 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2016 23:00:30 +0100 Subject: [PATCH 130/722] drop patch for XML-Bare that's specific to icc --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb index 652f0d5227..2ecf3ea45f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -419,7 +419,6 @@ exts_list = [ ('XML::Bare', '0.53', { 'source_tmpl': 'XML-Bare-0.53.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], - 'patches': ['XML-Bare-0.53_icc.patch'], }), ('Dist::CheckConflicts', '0.11', { 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', -- GitLab From 1de3ad9229b8db13719eb839de0939eca5ac260d Mon Sep 17 00:00:00 2001 From: perettig Date: Sat, 12 Mar 2016 12:29:15 +0100 Subject: [PATCH 131/722] dropping -XC suffix for Cray toolchains --- .../b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb | 22 ++++ .../b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb | 15 +++ .../b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb | 22 ++++ .../c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb | 22 ++++ .../c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb | 22 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb | 38 ++++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb | 38 ++++++ .../CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb | 48 ++++++++ .../c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb | 45 +++++++ ...ayCCE-2015.06-XC.eb => CrayCCE-2015.06.eb} | 2 +- ...ayCCE-2015.11-XC.eb => CrayCCE-2015.11.eb} | 2 +- ...ayGNU-2015.06-XC.eb => CrayGNU-2015.06.eb} | 2 +- ...ayGNU-2015.11-XC.eb => CrayGNU-2015.11.eb} | 2 +- ...tel-2015.06-XC.eb => CrayIntel-2015.06.eb} | 2 +- ...tel-2015.11-XC.eb => CrayIntel-2015.11.eb} | 2 +- .../f/flex/flex-2.5.39-CrayGNU-2015.06.eb | 14 +++ .../f/flex/flex-2.5.39-CrayGNU-2015.11.eb | 14 +++ .../GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb | 45 +++++++ .../GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb | 45 +++++++ .../GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb | 45 +++++++ .../h/HPL/HPL-2.1-CrayCCE-2015.06.eb | 22 ++++ .../h/HPL/HPL-2.1-CrayCCE-2015.11.eb | 22 ++++ .../h/HPL/HPL-2.1-CrayGNU-2015.06.eb | 18 +++ .../h/HPL/HPL-2.1-CrayGNU-2015.11.eb | 18 +++ .../h/HPL/HPL-2.1-CrayIntel-2015.06.eb | 18 +++ .../h/HPL/HPL-2.1-CrayIntel-2015.11.eb | 18 +++ .../JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb | 21 ++++ .../JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb | 21 ++++ .../JasPer-1.900.1-CrayIntel-2015.11.eb | 21 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb | 24 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb | 24 ++++ .../libreadline-6.3-CrayGNU-2015.06.eb | 30 +++++ .../libreadline-6.3-CrayGNU-2015.11.eb | 30 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb | 32 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb | 32 +++++ .../l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb | 33 +++++ .../m/M4/M4-1.4.17-CrayGNU-2015.06.eb | 23 ++++ .../m/M4/M4-1.4.17-CrayGNU-2015.11.eb | 23 ++++ .../n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb | 25 ++++ .../n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb | 25 ++++ .../n/ncurses/ncurses-5.9-CrayGNU-2015.06.eb | 34 ++++++ .../n/ncurses/ncurses-5.9-CrayGNU-2015.11.eb | 34 ++++++ .../ncurses/ncurses-5.9-CrayIntel-2015.11.eb | 34 ++++++ ...umpy-1.9.2-CrayGNU-2015.06-Python-2.7.9.eb | 26 ++++ ...umpy-1.9.2-CrayGNU-2015.11-Python-2.7.9.eb | 26 ++++ .../Python-2.7.9-CrayGNU-2015.06-bare.eb | 39 ++++++ .../p/Python/Python-2.7.9-CrayGNU-2015.06.eb | 115 ++++++++++++++++++ .../Python-2.7.9-CrayGNU-2015.11-bare.eb | 39 ++++++ .../p/Python/Python-2.7.9-CrayGNU-2015.11.eb | 115 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-2015.06.eb | 23 ++++ .../s/Szip/Szip-2.1-CrayGNU-2015.11.eb | 23 ++++ ...ipy-0.15.1-CrayGNU-2015.06-Python-2.7.9.eb | 19 +++ ...ipy-0.15.1-CrayGNU-2015.11-Python-2.7.9.eb | 19 +++ .../s/spglib/spglib-1.7.3-CrayGNU-2015.06.eb | 21 ++++ .../s/spglib/spglib-1.7.3-CrayGNU-2015.11.eb | 21 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb | 38 ++++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb | 38 ++++++ .../t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb | 38 ++++++ .../w/WRF/WRF-3.6.1-CrayGNU-2015.06-dmpar.eb | 41 +++++++ .../w/WRF/WRF-3.6.1-CrayGNU-2015.11-dmpar.eb | 41 +++++++ .../WRF/WRF-3.6.1-CrayIntel-2015.11-dmpar.eb | 41 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb | 22 ++++ .../z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb | 22 ++++ 65 files changed, 1827 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb rename easybuild/easyconfigs/c/CrayCCE/{CrayCCE-2015.06-XC.eb => CrayCCE-2015.06.eb} (96%) rename easybuild/easyconfigs/c/CrayCCE/{CrayCCE-2015.11-XC.eb => CrayCCE-2015.11.eb} (96%) rename easybuild/easyconfigs/c/CrayGNU/{CrayGNU-2015.06-XC.eb => CrayGNU-2015.06.eb} (96%) rename easybuild/easyconfigs/c/CrayGNU/{CrayGNU-2015.11-XC.eb => CrayGNU-2015.11.eb} (96%) rename easybuild/easyconfigs/c/CrayIntel/{CrayIntel-2015.06-XC.eb => CrayIntel-2015.06.eb} (96%) rename easybuild/easyconfigs/c/CrayIntel/{CrayIntel-2015.11-XC.eb => CrayIntel-2015.11.eb} (96%) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..1e373e5c59 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..fbde1c1bed --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..afe1e361bf --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..4907113147 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..3de7ff42c3 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..1f3739c57e --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb new file mode 100644 index 0000000000..7c87dffeab --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..428626aef1 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..1b2b44d855 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb new file mode 100644 index 0000000000..d34361f252 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb @@ -0,0 +1,48 @@ +# contributed by Luca Marsella (CSCS) +name = 'CP2K' +version = "3.0" +cudaversion = '7.0' +versionsuffix = '-cuda-%s' % cudaversion + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.2'), +] + +builddependencies = [ + ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test +runtest = False +# regression test reports failures +#ignore_regtest_fails = True + +# build type +type = 'psmp' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..e7bf9550c7 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb @@ -0,0 +1,45 @@ +# contributed by Luca Marsella (CSCS) +name = 'CP2K' +version = "3.0" + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.2'), +] + +builddependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test +runtest = False +# regression test reports failures +#ignore_regtest_fails = True + +# build type +type = 'psmp' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb rename to easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb index bf91772267..da34dc3b82 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayCCE' -version = '2015.06-XC' +version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb rename to easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb index dbf091ccf3..f6426373dd 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayCCE' -version = '2015.11-XC' +version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb rename to easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb index 0612076d5a..af4314daa9 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayGNU' -version = '2015.06-XC' +version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1506' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb index 370978db76..fdcd8836c8 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayGNU' -version = '2015.11-XC' +version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb rename to easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb index c80854490a..5d9b4c1609 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayIntel' -version = '2015.06-XC' +version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb similarity index 96% rename from easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb rename to easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb index cc105734db..8632b007b7 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11-XC.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb @@ -1,7 +1,7 @@ easyblock = 'CrayToolchain' name = 'CrayIntel' -version = '2015.11-XC' +version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: November 2015).\n""" diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..24e3dfb5dc --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..8c57faa309 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb new file mode 100644 index 0000000000..7fae7e2b3f --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/include && " + +dependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb new file mode 100644 index 0000000000..83b2732fb5 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " + +dependencies = [ + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb new file mode 100644 index 0000000000..350a3d6cfa --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " + +dependencies = [ + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb new file mode 100644 index 0000000000..934cc8d3eb --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '2015.06'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb new file mode 100644 index 0000000000..7a8e5a0800 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '2015.11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..4f4dbfc813 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..455f495e6e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb new file mode 100644 index 0000000000..00ee4facc9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.06'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb new file mode 100644 index 0000000000..651ae824ba --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..274dc46093 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..1a379efce9 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.eb new file mode 100644 index 0000000000..3cd71b46bf --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..173c7dbd1e --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..ef47d32bbf --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..883868add2 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..d828f262a5 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..d9d2ff8c6b --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..254367cee7 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..ae74d150b0 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb @@ -0,0 +1,33 @@ +# contributed by Luca Marsella (CSCS) +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..31c851b3d9 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..3010711346 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..a33090c4b6 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), +] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..c9ebfcb9f5 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fftw/3.3.4.5', EXTERNAL_MODULE), +] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..16fc4ff0ea --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..cb88b8202d --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11.eb new file mode 100644 index 0000000000..c1260d9ce2 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-Python-2.7.9.eb new file mode 100644 index 0000000000..aa3c00b163 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-Python-2.7.9.eb new file mode 100644 index 0000000000..5c8368180f --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb new file mode 100644 index 0000000000..92748077e8 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb @@ -0,0 +1,39 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..21613bcfb7 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb new file mode 100644 index 0000000000..f7679002a1 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb @@ -0,0 +1,39 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..9958308892 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..de900f73b2 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True, } + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..58f5db7a33 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True, } + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-Python-2.7.9.eb new file mode 100644 index 0000000000..bec11c9016 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-Python-2.7.9.eb new file mode 100644 index 0000000000..35ad3eac24 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..7601dde601 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..0395e331ec --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..bf01430fff --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..57a30b1d87 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb new file mode 100644 index 0000000000..558feb7579 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-dmpar.eb new file mode 100644 index 0000000000..c88ec72408 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-dmpar.eb new file mode 100644 index 0000000000..ab4cacf6da --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-dmpar.eb new file mode 100644 index 0000000000..ac5084ad2d --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayIntel', 'version': '2015.11'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb new file mode 100644 index 0000000000..9daa7bba81 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.06'} +toolchainopts = {'pic': True, } + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..ec75812a65 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True, } + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From bbb4bf36f5f8bcd852aade02c94232fdaa899bbf Mon Sep 17 00:00:00 2001 From: perettig Date: Sat, 12 Mar 2016 12:32:09 +0100 Subject: [PATCH 132/722] delete old -XC files --- .../b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb | 22 ---- .../b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb | 22 ---- .../b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb | 15 --- .../b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb | 15 --- .../c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb | 22 ---- .../c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb | 22 ---- .../CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb | 22 ---- .../c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb | 38 ------ .../c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb | 38 ------ .../CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb | 48 -------- .../c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb | 45 ------- .../f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb | 14 --- .../f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb | 14 --- .../GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb | 45 ------- .../GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb | 45 ------- .../GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb | 45 ------- .../h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb | 22 ---- .../h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb | 22 ---- .../h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb | 18 --- .../h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb | 18 --- .../h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb | 18 --- .../h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb | 18 --- .../JasPer-1.900.1-CrayGNU-2015.06-XC.eb | 21 ---- .../JasPer-1.900.1-CrayGNU-2015.11-XC.eb | 21 ---- .../JasPer-1.900.1-CrayIntel-2015.11-XC.eb | 21 ---- .../Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb | 24 ---- .../Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb | 24 ---- .../libreadline-6.3-CrayGNU-2015.06-XC.eb | 30 ----- .../libreadline-6.3-CrayGNU-2015.11-XC.eb | 30 ----- .../l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb | 32 ----- .../l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb | 32 ----- .../l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb | 33 ----- .../m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb | 23 ---- .../m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb | 23 ---- .../n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb | 25 ---- .../n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb | 25 ---- .../ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb | 34 ------ .../ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb | 34 ------ .../ncurses-5.9-CrayIntel-2015.11-XC.eb | 34 ------ ...y-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb | 26 ---- ...y-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb | 26 ---- .../Python-2.7.9-CrayGNU-2015.06-XC-bare.eb | 39 ------ .../Python/Python-2.7.9-CrayGNU-2015.06-XC.eb | 115 ------------------ .../Python-2.7.9-CrayGNU-2015.11-XC-bare.eb | 39 ------ .../Python/Python-2.7.9-CrayGNU-2015.11-XC.eb | 115 ------------------ .../s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb | 23 ---- .../s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb | 23 ---- ...-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb | 19 --- ...-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb | 19 --- .../spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb | 21 ---- .../spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb | 21 ---- .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb | 38 ------ .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb | 38 ------ .../tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb | 38 ------ .../WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb | 41 ------- .../WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb | 41 ------- .../WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb | 41 ------- .../z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb | 22 ---- .../z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb | 22 ---- 59 files changed, 1821 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb delete mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb delete mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb delete mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb delete mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb delete mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 77bb4a043c..0000000000 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.0.2' - -homepage = 'http://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [('M4', '1.4.17')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb deleted file mode 100644 index cfb18be138..0000000000 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.0.2' - -homepage = 'http://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [('M4', '1.4.17')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs': [], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 5b74aeb4ae..0000000000 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,15 +0,0 @@ -name = 'bzip2' -version = '1.0.6' - -homepage = 'http://www.bzip.org/' -description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically - compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical - compressors), whilst being around twice as fast at compression and six times faster at decompression.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.bzip.org/%(version)s'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 5666a2e9f5..0000000000 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,15 +0,0 @@ -name = 'bzip2' -version = '1.0.6' - -homepage = 'http://www.bzip.org/' -description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically - compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical - compressors), whilst being around twice as fast at compression and six times faster at decompression.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.bzip.org/%(version)s'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb deleted file mode 100644 index d4b9c66352..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.2.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 1a73916b52..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.2.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb deleted file mode 100644 index 8fe0d6e4d8..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.2.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb deleted file mode 100644 index c1c02c3bcf..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'CP2K' -version = '2.6.0' - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.1'), -] - -builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test reports failures -ignore_regtest_fails = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 18250df781..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'CP2K' -version = '2.6.0' - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.1'), -] - -builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test reports failures -ignore_regtest_fails = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb deleted file mode 100644 index aeb506b2a1..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC-cuda-7.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -# contributed by Luca Marsella (CSCS) -name = 'CP2K' -version = "3.0" -cudaversion = '7.0' -versionsuffix = '-cuda-%s' % cudaversion - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.2'), -] - -builddependencies = [ - ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE), - ('fftw/3.3.4.3', EXTERNAL_MODULE), - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test -runtest = False -# regression test reports failures -#ignore_regtest_fails = True - -# build type -type = 'psmp' - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 55e00d968f..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,45 +0,0 @@ -# contributed by Luca Marsella (CSCS) -name = 'CP2K' -version = "3.0" - -homepage = 'http://www.cp2k.org/' -description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular - simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different - methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and - classical pair and many-body potentials. """ - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [SOURCEFORGE_SOURCE] - -patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] - -dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.2'), -] - -builddependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), - ('flex', '2.5.39'), - ('Bison', '3.0.2'), -] - -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 - -# regression test -runtest = False -# regression test reports failures -#ignore_regtest_fails = True - -# build type -type = 'psmp' - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb deleted file mode 100644 index d9b2e6f439..0000000000 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,14 +0,0 @@ -name = 'flex' -version = '2.5.39' - -homepage = 'http://flex.sourceforge.net/' -description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 7fbee438c5..0000000000 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,14 +0,0 @@ -name = 'flex' -version = '2.5.39' - -homepage = 'http://flex.sourceforge.net/' -description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb deleted file mode 100644 index eb693a5ca3..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-XC-mpi.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.7' -versionsuffix = '-mpi' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'usempi': True} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " -preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/include && " - -dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), -] - -builddependencies = [('CMake', '3.2.2')] - -runtest = False - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb deleted file mode 100644 index 7d022ac778..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-XC-mpi.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.7' -versionsuffix = '-mpi' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'usempi': True} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " -preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " - -dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), -] - -builddependencies = [('CMake', '3.2.2')] - -runtest = False - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb deleted file mode 100644 index 492e226263..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-XC-mpi.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.7' -versionsuffix = '-mpi' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'usempi': True} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " -preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " - -dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), -] - -builddependencies = [('CMake', '3.2.2')] - -runtest = False - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb deleted file mode 100644 index 845802b504..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayCCE', 'version': '2015.06-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -patches = [ - # fix Make dependencies, so parallel build also works - 'HPL_parallel-make.patch', - 'HPL-2.1_LINKER-ld.patch', -] - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb deleted file mode 100644 index f4a0256f79..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayCCE', 'version': '2015.11-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -patches = [ - # fix Make dependencies, so parallel build also works - 'HPL_parallel-make.patch', - 'HPL-2.1_LINKER-ld.patch', -] - -parallel = 1 - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb deleted file mode 100644 index fe0de8812c..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb deleted file mode 100644 index ecd5998b8d..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb deleted file mode 100644 index 32e943a8d6..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06-XC.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.06-XC'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb deleted file mode 100644 index 370ce49b4c..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 057b6423c3..0000000000 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'JasPer' -version = '1.900.1' - -homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' -description = """The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_ZIP] -source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] - -sanity_check_paths = { - 'files': ["bin/jasper", "lib/libjasper.a"], - 'dirs': ["include"], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb deleted file mode 100644 index b3d235faba..0000000000 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'JasPer' -version = '1.900.1' - -homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' -description = """The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_ZIP] -source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] - -sanity_check_paths = { - 'files': ["bin/jasper", "lib/libjasper.a"], - 'dirs': ["include"], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb deleted file mode 100644 index 45bc1007dd..0000000000 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'JasPer' -version = '1.900.1' - -homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' -description = """The JasPer Project is an open-source initiative to provide a free - software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_ZIP] -source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] - -sanity_check_paths = { - 'files': ["bin/jasper", "lib/libjasper.a"], - 'dirs': ["include"], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 8c50a3c766..0000000000 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'Libint' -version = '1.1.4' - -homepage = 'https://sourceforge.net/p/libint/' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'opt': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') - -configopts = "--enable-deriv --enable-r12" - -sanity_check_paths = { - 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + - ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + - ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb deleted file mode 100644 index ba7eabefb4..0000000000 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'Libint' -version = '1.1.4' - -homepage = 'https://sourceforge.net/p/libint/' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'opt': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') - -configopts = "--enable-deriv --enable-r12" - -sanity_check_paths = { - 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + - ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + - ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 86d9535460..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '6.3' - -homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' -description = """The GNU Readline library provides a set of functions for use by applications that - allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. - The Readline library includes additional functions to maintain a list of previously-entered command lines, - to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '5.9')] - -# for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" - -sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 9f6f591568..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '6.3' - -homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' -description = """The GNU Readline library provides a set of functions for use by applications that - allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. - The Readline library includes additional functions to maintain a list of previously-entered command lines, - to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '5.9')] - -# for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" - -sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 3ef89d660d..0000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '2.2.1' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'opt': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] - -configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' - -# From the libxc mailing list -# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -# a fully working testsuite soon (unless someone wants to volunteer to do -# it, of course ) In the meantime, unless the majority of the tests -# fail, your build should be fine. -#runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc.a'], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb deleted file mode 100644 index bfd88b3c4b..0000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '2.2.1' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'opt': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] - -configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' - -# From the libxc mailing list -# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -# a fully working testsuite soon (unless someone wants to volunteer to do -# it, of course ) In the meantime, unless the majority of the tests -# fail, your build should be fine. -#runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc.a'], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 99ad1db263..0000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,33 +0,0 @@ -# contributed by Luca Marsella (CSCS) -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '2.2.2' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'opt': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] - -configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' - -# From the libxc mailing list -# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -# a fully working testsuite soon (unless someone wants to volunteer to do -# it, of course ) In the meantime, unless the majority of the tests -# fail, your build should be fine. -#runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc.a', 'lib/libxc.so'], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 68ee7aa23b..0000000000 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'M4' -version = '1.4.17' - -homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -configopts = "--enable-cxx" - -sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb deleted file mode 100644 index fd7cafa798..0000000000 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'M4' -version = '1.4.17' - -homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -configopts = "--enable-cxx" - -sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb deleted file mode 100644 index f016964748..0000000000 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'NFFT' -version = '3.3.0' - -homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' -description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine - library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more - dimensions, of arbitrary input size, and of complex data.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), -] - -sanity_check_paths = { - 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 10957199be..0000000000 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'NFFT' -version = '3.3.0' - -homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' -description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine - library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more - dimensions, of arbitrary input size, and of complex data.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), -] - -sanity_check_paths = { - 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb deleted file mode 100644 index f11ad3873e..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 0c15e725f4..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb deleted file mode 100644 index 6caf9a9b85..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb deleted file mode 100644 index 09f3884a76..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.06-XC-Python-2.7.9.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'numpy' -version = '1.9.2' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['numpy-1.8.0-mkl.patch'] - -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb deleted file mode 100644 index 91375139ee..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-2015.11-XC-Python-2.7.9.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'numpy' -version = '1.9.2' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['numpy-1.8.0-mkl.patch'] - -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb deleted file mode 100644 index ae58dbb498..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC-bare.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'Python' -version = '2.7.9' -versionsuffix = '-bare' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True, 'opt': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -# bare installation: no extensions included -exts_list = [] - -buildopts = 'LINKCC="$CC -dynamic"' - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb deleted file mode 100644 index d2018b8970..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,115 +0,0 @@ -name = 'Python' -version = '2.7.9' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.9.1' -scipyversion = '0.14.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -buildopts = 'LINKCC="$CC -dynamic"' - -# order is important! -# package versions updated Jan 19th 2015 -exts_list = [ - ('setuptools', '11.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.4.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.13', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), -] - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb deleted file mode 100644 index f91af70f07..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC-bare.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'Python' -version = '2.7.9' -versionsuffix = '-bare' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True, 'opt': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -# bare installation: no extensions included -exts_list = [] - -buildopts = 'LINKCC="$CC -dynamic"' - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb deleted file mode 100644 index da85447313..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,115 +0,0 @@ -name = 'Python' -version = '2.7.9' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.9.1' -scipyversion = '0.14.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] - -buildopts = 'LINKCC="$CC -dynamic"' - -# order is important! -# package versions updated Jan 19th 2015 -exts_list = [ - ('setuptools', '11.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.4.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.13', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), -] - -sanity_check_commands = [ - ('python', '--version'), - ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works - ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another - ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) - ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb deleted file mode 100644 index a075d53839..0000000000 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1' - -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' -description = "Szip compression software, providing lossless compression of scientific data" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True, } - -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 6340c63211..0000000000 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1' - -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' -description = "Szip compression software, providing lossless compression of scientific data" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True, } - -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb deleted file mode 100644 index b47cc99c57..0000000000 --- a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.06-XC-Python-2.7.9.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'scipy' -version = '0.15.1' -versionsuffix = '-Python-2.7.9' - -homepage = 'http://www.scipy.org' -description = """SciPy is a collection of mathematical algorithms and convenience - functions built on the Numpy extension for Python.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True} - -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('numpy', '1.9.2', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb deleted file mode 100644 index b69de1aa3b..0000000000 --- a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-2015.11-XC-Python-2.7.9.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'scipy' -version = '0.15.1' -versionsuffix = '-Python-2.7.9' - -homepage = 'http://www.scipy.org' -description = """SciPy is a collection of mathematical algorithms and convenience - functions built on the Numpy extension for Python.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True} - -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('numpy', '1.9.2', versionsuffix), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb deleted file mode 100644 index 68086c7c98..0000000000 --- a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'spglib' -version = '1.7.3' - -homepage = 'http://spglib.sourceforge.net/' -description = """Spglib is a C library for finding and handling crystal symmetries.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -start_dir = '%(name)s-%(version)s' - -sanity_check_paths = { - 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], - 'dirs': ['include/spglib'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb deleted file mode 100644 index bdb5c45a5a..0000000000 --- a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'spglib' -version = '1.7.3' - -homepage = 'http://spglib.sourceforge.net/' -description = """Spglib is a C library for finding and handling crystal symmetries.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -start_dir = '%(name)s-%(version)s' - -sanity_check_paths = { - 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], - 'dirs': ['include/spglib'], -} - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb deleted file mode 100644 index c5db50a961..0000000000 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -# Authors:: Valentin Plugaru -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html -## -easyblock = 'ConfigureMake' - -name = 'tcsh' -version = '6.18.01' - -homepage = 'http://www.tcsh.org' -description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). - It is a command language interpreter usable both as an interactive login shell and a shell script command - processor. It includes a command-line editor, programmable word completion, spelling correction, a history - mechanism, job control and a C-like syntax.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.astron.com/pub/%(namelower)s', - 'ftp://ftp.astron.com/pub/%(namelower)s/old', -] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/tcsh"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 3b456bd5d5..0000000000 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -# Authors:: Valentin Plugaru -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html -## -easyblock = 'ConfigureMake' - -name = 'tcsh' -version = '6.18.01' - -homepage = 'http://www.tcsh.org' -description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). - It is a command language interpreter usable both as an interactive login shell and a shell script command - processor. It includes a command-line editor, programmable word completion, spelling correction, a history - mechanism, job control and a C-like syntax.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.astron.com/pub/%(namelower)s', - 'ftp://ftp.astron.com/pub/%(namelower)s/old', -] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/tcsh"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb deleted file mode 100644 index df83e70f3b..0000000000 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11-XC.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit -# Authors:: Valentin Plugaru -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html -## -easyblock = 'ConfigureMake' - -name = 'tcsh' -version = '6.18.01' - -homepage = 'http://www.tcsh.org' -description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). - It is a command language interpreter usable both as an interactive login shell and a shell script command - processor. It includes a command-line editor, programmable word completion, spelling correction, a history - mechanism, job control and a C-like syntax.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.astron.com/pub/%(namelower)s', - 'ftp://ftp.astron.com/pub/%(namelower)s/old', -] - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ["bin/tcsh"], - 'dirs': [] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb deleted file mode 100644 index 0b7fd5cfb3..0000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.06-XC-dmpar.eb +++ /dev/null @@ -1,41 +0,0 @@ -name = 'WRF' -version = '3.6.1' - -homepage = 'http://www.wrf-model.org' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -sources = ['%(name)sV%(version)s.TAR.gz'] -source_urls = [ - 'http://www2.mmm.ucar.edu/wrf/src/', - 'http://www.mmm.ucar.edu/wrf/src/', -] - -# csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] - -dependencies = [ - ('JasPer', '1.900.1'), - ('cray-netcdf/4.3.2', EXTERNAL_MODULE), - ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), -] - -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-3.6.1_known_problems.patch', - 'WRF_tests_limit-runtimes.patch', -] - -# limit parallel build to 20 -maxparallel = 20 - -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -runtest = False - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb deleted file mode 100644 index d353e6742c..0000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-2015.11-XC-dmpar.eb +++ /dev/null @@ -1,41 +0,0 @@ -name = 'WRF' -version = '3.6.1' - -homepage = 'http://www.wrf-model.org' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -sources = ['%(name)sV%(version)s.TAR.gz'] -source_urls = [ - 'http://www2.mmm.ucar.edu/wrf/src/', - 'http://www.mmm.ucar.edu/wrf/src/', -] - -# csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] - -dependencies = [ - ('JasPer', '1.900.1'), - ('cray-netcdf/4.3.2', EXTERNAL_MODULE), - ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), -] - -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-3.6.1_known_problems.patch', - 'WRF_tests_limit-runtimes.patch', -] - -# limit parallel build to 20 -maxparallel = 20 - -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -runtest = False - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb deleted file mode 100644 index dc552a3235..0000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayIntel-2015.11-XC-dmpar.eb +++ /dev/null @@ -1,41 +0,0 @@ -name = 'WRF' -version = '3.6.1' - -homepage = 'http://www.wrf-model.org' -description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale - numerical weather prediction system designed to serve both operational forecasting and atmospheric - research needs.""" - -toolchain = {'name': 'CrayIntel', 'version': '2015.11-XC'} -toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 - -sources = ['%(name)sV%(version)s.TAR.gz'] -source_urls = [ - 'http://www2.mmm.ucar.edu/wrf/src/', - 'http://www.mmm.ucar.edu/wrf/src/', -] - -# csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] - -dependencies = [ - ('JasPer', '1.900.1'), - ('cray-netcdf/4.3.2', EXTERNAL_MODULE), - ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), -] - -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-3.6.1_known_problems.patch', - 'WRF_tests_limit-runtimes.patch', -] - -# limit parallel build to 20 -maxparallel = 20 - -buildtype = "dmpar" -versionsuffix = '-%s' % buildtype - -runtest = False - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb deleted file mode 100644 index fbc74998eb..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.8' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.06-XC'} -toolchainopts = {'pic': True, } - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb deleted file mode 100644 index 0c6915d7cd..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.8' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'pic': True, } - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' -- GitLab From 1a04d6640a63dcb22c3ca78d7ce4c477867f8572 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 13 Mar 2016 20:50:25 +0000 Subject: [PATCH 133/722] Add packed binary version of sratoolkit 2.5.7 --- .../s/sratoolkit/sratoolkit-2.5.7.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb diff --git a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb new file mode 100644 index 0000000000..e8e5e37a6b --- /dev/null +++ b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb @@ -0,0 +1,34 @@ +easyblock = 'PackedBinary' + +name = 'sratoolkit' +version = '2.5.7' + +homepage = 'http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] +sources = ['sratoolkit.%(version)s-centos_linux64.tar.gz'] + +executables = [ +'abi-dump*', 'abi-load*', 'align-info*', 'bam-load*', 'blastn_vdb*', 'cache-mgr*', +'cg-load*', 'fastq-dump*', 'fastq-load*', 'helicos-load*', 'illumina-dump*', +'illumina-load*', 'kar*', 'kdbmeta*', 'latf-load*', 'ncbi', 'pacbio-load*', +'prefetch*', 'rcexplain*', 'remote-fuser*', 'sam-dump*', 'sff-dump*', +'sff-load*', 'sra-kar*', 'sra-pileup*', 'sra-sort*', 'sra-stat*', 'srapath*', +'srf-load*', 'tblastn_vdb*', 'test-sra*', 'vdb-config*', 'vdb-copy*', +'vdb-decrypt*', 'vdb-dump*', 'vdb-encrypt*', 'vdb-lock*', 'vdb-passwd*', +'vdb-unlock*', 'vdb-validate*', +] + +files_to_copy = [('*', 'bin')] + +sanity_check_paths = { + 'files': ['bin/abi-dump', 'bin/illumina-load', 'bin/srf-load', ], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From c09c304722a69796d45d2678918508534f225b37 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 13 Mar 2016 20:53:24 +0000 Subject: [PATCH 134/722] Add proper header with attribution --- easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb index e8e5e37a6b..fc210435ee 100644 --- a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb +++ b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb @@ -1,3 +1,10 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute +# Based on work by npklein + easyblock = 'PackedBinary' name = 'sratoolkit' -- GitLab From 9750d399b67a70e27e331d3ed0227bf30d373ea5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 13:55:10 +0100 Subject: [PATCH 135/722] include pandas as extension in Python 3.5.1 easyconfigs --- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index ec80435d9b..782d02fe62 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -107,6 +107,9 @@ exts_list = [ ('netaddr', '0.7.18', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index aa7a7d9034..5dcd8c848b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -111,6 +111,9 @@ exts_list = [ ('netaddr', '0.7.18', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' -- GitLab From dc22f84516afbdee12bbc87d59077c30d83704a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 15:10:34 +0200 Subject: [PATCH 136/722] modify easyconfig scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb, modify easyconfig matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb --- ...tplotlib-1.5.1-intel-2016a-Python-3.5.1.eb | 45 +++++++++++++++++++ ...t-learn-0.17.1-intel-2016a-Python-3.5.1.eb | 30 +++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..2c2c674d2c --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c "import %(ext_name)s"', '') + +dependencies = [ + ('Python', '3.5.1'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..f49a608d87 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.17.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From a22ef3361ebc08e4296092d559b97071e024068d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 17:57:47 +0200 Subject: [PATCH 137/722] add easyconfig ADF-2016.101.eb --- easybuild/easyconfigs/a/ADF/ADF-2016.101.eb | 31 +++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/ADF/ADF-2016.101.eb diff --git a/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb b/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb new file mode 100644 index 0000000000..5fe5e14c14 --- /dev/null +++ b/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'ADF' +version = '2016.101' + +homepage = 'http://www.scm.com/ADF/' +description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and + predict chemical structure and reactivity with density functional theory (DFT).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['adf%(version)s.pc64_linux.intelmpi.tgz'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +modextravars = { + 'ADFHOME': '%(installdir)s', + 'ADFBIN': '%(installdir)s/bin', + 'ADFRESOURCES': '%(installdir)s/atomicdata', +} + +modloadmsg = "These environment variables need to be defined before using ADF:\n" +modloadmsg += " * $SCMLICENSE: path to ADF license file\n" +modloadmsg += " * $SCM_TMPDIR: path to user scratch directory" + +moduleclass = 'chem' -- GitLab From 600a222f07887960db797217fe7d058dfeb7a046 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 18:13:18 +0200 Subject: [PATCH 138/722] add easyconfig statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb --- ...tsmodels-0.6.1-intel-2016a-Python-3.5.1.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..a2ab69cdf5 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,40 @@ +easyblock = 'Bundle' + +name = 'statsmodels' +version = '0.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/statsmodels' +description = """Statsmodels is a Python package that provides a complement to scipy for statistical computations + including descriptive statistics and estimation and inference for statistical models.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.1'), +] + +exts_list = [ + ('patsy', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], + 'source_tmpl': 'patsy-%(version)s.zip', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'math' -- GitLab From 7c545ed144d07424dff4f16fffbb9dc94b1f950d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 14 Mar 2016 17:14:09 +0000 Subject: [PATCH 139/722] Fix indent and sanity check --- .../s/sratoolkit/sratoolkit-2.5.7.eb | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb index fc210435ee..da9654c11e 100644 --- a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb +++ b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb @@ -21,21 +21,21 @@ source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s-centos_linux64.tar.gz'] executables = [ -'abi-dump*', 'abi-load*', 'align-info*', 'bam-load*', 'blastn_vdb*', 'cache-mgr*', -'cg-load*', 'fastq-dump*', 'fastq-load*', 'helicos-load*', 'illumina-dump*', -'illumina-load*', 'kar*', 'kdbmeta*', 'latf-load*', 'ncbi', 'pacbio-load*', -'prefetch*', 'rcexplain*', 'remote-fuser*', 'sam-dump*', 'sff-dump*', -'sff-load*', 'sra-kar*', 'sra-pileup*', 'sra-sort*', 'sra-stat*', 'srapath*', -'srf-load*', 'tblastn_vdb*', 'test-sra*', 'vdb-config*', 'vdb-copy*', -'vdb-decrypt*', 'vdb-dump*', 'vdb-encrypt*', 'vdb-lock*', 'vdb-passwd*', -'vdb-unlock*', 'vdb-validate*', + 'abi-dump*', 'abi-load*', 'align-info*', 'bam-load*', 'blastn_vdb*', 'cache-mgr*', + 'cg-load*', 'fastq-dump*', 'fastq-load*', 'helicos-load*', 'illumina-dump*', + 'illumina-load*', 'kar*', 'kdbmeta*', 'latf-load*', 'ncbi', 'pacbio-load*', + 'prefetch*', 'rcexplain*', 'remote-fuser*', 'sam-dump*', 'sff-dump*', + 'sff-load*', 'sra-kar*', 'sra-pileup*', 'sra-sort*', 'sra-stat*', 'srapath*', + 'srf-load*', 'tblastn_vdb*', 'test-sra*', 'vdb-config*', 'vdb-copy*', + 'vdb-decrypt*', 'vdb-dump*', 'vdb-encrypt*', 'vdb-lock*', 'vdb-passwd*', + 'vdb-unlock*', 'vdb-validate*', ] files_to_copy = [('*', 'bin')] sanity_check_paths = { - 'files': ['bin/abi-dump', 'bin/illumina-load', 'bin/srf-load', ], - 'dirs': [] + 'files': [], + 'dirs': ['bin'] } moduleclass = 'bio' -- GitLab From 24f917cdef4c9a335c64052ea227ee67623450fc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 14 Mar 2016 17:37:12 +0000 Subject: [PATCH 140/722] Remove executables and add detail to sanity check --- .../s/sratoolkit/sratoolkit-2.5.7.eb | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb index da9654c11e..b3d358e4a3 100644 --- a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb +++ b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb @@ -20,22 +20,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s-centos_linux64.tar.gz'] -executables = [ - 'abi-dump*', 'abi-load*', 'align-info*', 'bam-load*', 'blastn_vdb*', 'cache-mgr*', - 'cg-load*', 'fastq-dump*', 'fastq-load*', 'helicos-load*', 'illumina-dump*', - 'illumina-load*', 'kar*', 'kdbmeta*', 'latf-load*', 'ncbi', 'pacbio-load*', - 'prefetch*', 'rcexplain*', 'remote-fuser*', 'sam-dump*', 'sff-dump*', - 'sff-load*', 'sra-kar*', 'sra-pileup*', 'sra-sort*', 'sra-stat*', 'srapath*', - 'srf-load*', 'tblastn_vdb*', 'test-sra*', 'vdb-config*', 'vdb-copy*', - 'vdb-decrypt*', 'vdb-dump*', 'vdb-encrypt*', 'vdb-lock*', 'vdb-passwd*', - 'vdb-unlock*', 'vdb-validate*', -] - -files_to_copy = [('*', 'bin')] - sanity_check_paths = { - 'files': [], - 'dirs': ['bin'] + 'files': ['bin/abi-load', 'bin/fastq-dump', 'bin/sff-load', 'bin/vdb-dump'], + 'dirs': [] } moduleclass = 'bio' -- GitLab From 594901c38692154ba44bae343882354bc7c0af7d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 19:34:41 +0100 Subject: [PATCH 141/722] stick to binutils 2.25 for now --- .../b/binutils/binutils-2.26-GCCcore-4.9.3.eb | 41 ------------------- ...26.eb => icc-2016.2.181-GCC-4.9.3-2.25.eb} | 2 +- ... => iccifort-2016.2.181-GCC-4.9.3-2.25.eb} | 2 +- ....eb => ifort-2016.2.181-GCC-4.9.3-2.25.eb} | 2 +- ....26.eb => iimpi-2016.02-GCC-4.9.3-2.25.eb} | 2 +- ...1.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb} | 2 +- ...181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb} | 2 +- .../i/intel/intel-2016.02-GCC-4.9.eb | 2 +- 8 files changed, 7 insertions(+), 48 deletions(-) delete mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb rename easybuild/easyconfigs/i/icc/{icc-2016.2.181-GCC-4.9.3-2.26.eb => icc-2016.2.181-GCC-4.9.3-2.25.eb} (98%) rename easybuild/easyconfigs/i/iccifort/{iccifort-2016.2.181-GCC-4.9.3-2.26.eb => iccifort-2016.2.181-GCC-4.9.3-2.25.eb} (93%) rename easybuild/easyconfigs/i/ifort/{ifort-2016.2.181-GCC-4.9.3-2.26.eb => ifort-2016.2.181-GCC-4.9.3-2.25.eb} (98%) rename easybuild/easyconfigs/i/iimpi/{iimpi-2016.02-GCC-4.9.3-2.26.eb => iimpi-2016.02-GCC-4.9.3-2.25.eb} (94%) rename easybuild/easyconfigs/i/imkl/{imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb => imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb} (95%) rename easybuild/easyconfigs/i/impi/{impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb => impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb} (99%) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb deleted file mode 100644 index 0d3fdd2d17..0000000000 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.3.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'binutils' -version = '2.26' - -homepage = 'http://directory.fsf.org/project/binutils/' -description = "binutils: GNU binary utilities" - -toolchain = {'name': 'GCCcore', 'version': '4.9.3'} - -sources = [SOURCE_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [ - ('flex', '2.6.0'), - ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep - ('zlib', '1.2.8'), - # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) -] - -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb similarity index 98% rename from easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index ec73b70b03..569030c764 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -13,7 +13,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update checksums = ['d6f8529a44231e427219c8e025dec3b2'] gccver = '4.9.3' -binutilsver = '2.26' +binutilsver = '2.25' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb similarity index 93% rename from easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 93577bed54..871fae395a 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ easyblock = "Toolchain" name = 'iccifort' version = '2016.2.181' -versionsuffix = '-GCC-4.9.3-2.26' +versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb similarity index 98% rename from easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index c55e928942..01be1aa191 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -13,7 +13,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] gccver = '4.9.3' -binutilsver = '2.26' +binutilsver = '2.25' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb similarity index 94% rename from easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb index 0be81ea753..3d1b981714 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ easyblock = "Toolchain" name = 'iimpi' version = '2016.02' -versionsuffix = '-GCC-4.9.3-2.26' +versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb similarity index 95% rename from easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index 78baf11191..34b7b8bb07 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-4.9.3-2.26'} +toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['536dbd82896d6facc16de8f961d17d65'] diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb similarity index 99% rename from easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb rename to easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 147e9c1ec1..d3526d68e5 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -8,7 +8,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" -toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-4.9.3-2.26'} +toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-4.9.3-2.25'} sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb index 955db91710..41552f25a9 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.2.181' gccver = '%s.3' % gcc_maj_min -binutilsver = '2.26' +binutilsver = '2.25' gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ ('GCCcore', gccver), -- GitLab From a1164904bfbae01fbb12a988aaef505d6dc5bf0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Mar 2016 20:39:31 +0100 Subject: [PATCH 142/722] fix binutils version in flex easyconfig --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb index 5a3de111fc..4015f41291 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -14,7 +14,7 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] dependencies = [('Bison', '3.0.4')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.25', '', True)] parallel = 1 -- GitLab From 83cfd2deaf27fe0045109af043a5552e36fe47de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 10:33:31 +0100 Subject: [PATCH 143/722] use HOME constant in new icc/ifort/imkl/impi easyconfigs --- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb | 4 +--- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb | 4 +--- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb | 4 +--- .../impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 3 +-- 4 files changed, 4 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index 569030c764..9338983477 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -28,8 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index 01be1aa191..5db05e1948 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -28,8 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index 34b7b8bb07..53630f7111 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -16,9 +16,7 @@ checksums = ['536dbd82896d6facc16de8f961d17d65'] dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index d3526d68e5..d059a83720 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -16,8 +16,7 @@ checksums = ['1c14656859d48bf8b90c71dace2a977b'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From d8bf857a307113e1541033bfc4af67cbef5a358f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 10:35:31 +0100 Subject: [PATCH 144/722] use HOME constant in new icc/ifort/imkl/impi easyconfigs --- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 4 +--- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 4 +--- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 4 +--- .../impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 3 +-- 4 files changed, 4 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index 080cfccc9a..fad8d6d04d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,8 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 3ee926155e..16a589b7f3 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,8 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index 74cc4cff3a..dd75357fc5 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -16,9 +16,7 @@ checksums = ['536dbd82896d6facc16de8f961d17d65'] dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index ef29e9af70..faa72cc81c 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -16,8 +16,7 @@ checksums = ['1c14656859d48bf8b90c71dace2a977b'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From 1f16832a0cfc461c45b7c35a796f53db2ab4b4c6 Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 11:44:31 +0100 Subject: [PATCH 145/722] QuickFF and Yaff for DEFNET --- ...QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb | 34 ++++++++++++++++++ ....develop.2.13-intel-2015b-Python-2.7.10.eb | 35 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..e48df83b5c --- /dev/null +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'QuickFF' +version = '2.0.1' + +homepage = 'http://molmod.github.io/QuickFF/' +description = """QuickFF is a Python package developed at the Center for +Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio +calculations.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/molmod/QuickFF/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.5.0', versionsuffix), + ('molmod', '1.1', versionsuffix), + ('yaff', 'thesissven2.13', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..36a2dc281d --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'yaff' +version = '1.0.develop.2.13' + +homepage = 'http://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.10' + +hdf5ver = '1.8.15-patch1' +versionsuffix = '-Python-%s-HDF5-%s-serial' %(pyver, hdf5ver) + +dependencies = [ + ('Python', pyver), + ('h5py', '2.5.0', versionsuffix), + ('molmod', '1.1', '-Python-%s' %(pyver)), +] + +options = {'modulename': name} +#runtest = 'python setup.py build_ext -i; nosetests -v' + + +pyshortver = ".".join(pyver.split(".")[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver, name)] +} + +moduleclass = 'chem' -- GitLab From 4143001890fac7735da939e011118aed9d4c120b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 13:07:31 +0100 Subject: [PATCH 146/722] add missing '/' --- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index 9338983477..4d0d75afae 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index 5db05e1948..ffe995c4ac 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index 53630f7111..91dcce3df9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -16,7 +16,7 @@ checksums = ['536dbd82896d6facc16de8f961d17d65'] dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index d059a83720..845f7631f8 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -16,7 +16,7 @@ checksums = ['1c14656859d48bf8b90c71dace2a977b'] dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From d8b707a6e21dba177b222b93322c3798dd0677ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 13:09:20 +0100 Subject: [PATCH 147/722] add missing '/' --- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index fad8d6d04d..5c1c6d97c5 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 16a589b7f3..5844c8abd9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index dd75357fc5..d1edf0b015 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -16,7 +16,7 @@ checksums = ['536dbd82896d6facc16de8f961d17d65'] dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index faa72cc81c..eaf9a3b7a7 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -16,7 +16,7 @@ checksums = ['1c14656859d48bf8b90c71dace2a977b'] dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From 4e9120dea53da6a178d82c6c2c61f56300116ace Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 13:50:41 +0100 Subject: [PATCH 148/722] Fix yaff version in quickff eb, fix yaff eb filename and fix yaff nosetests --- ...QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb | 2 +- ....develop.2.13-intel-2015b-Python-2.7.10.eb | 35 ------------------- 2 files changed, 1 insertion(+), 36 deletions(-) delete mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb index e48df83b5c..5d737222c9 100644 --- a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb @@ -23,7 +23,7 @@ dependencies = [ (python, pythonversion), ('matplotlib', '1.5.0', versionsuffix), ('molmod', '1.1', versionsuffix), - ('yaff', 'thesissven2.13', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) + ('yaff', '1.0.develop.2.13', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb deleted file mode 100644 index 36a2dc281d..0000000000 --- a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.13-intel-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = "PythonPackage" - -name = 'yaff' -version = '1.0.develop.2.13' - -homepage = 'http://molmod.github.io/yaff/' -description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" - -toolchain = {'name': 'intel', 'version': '2015b'} - -source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] - -pyver = '2.7.10' - -hdf5ver = '1.8.15-patch1' -versionsuffix = '-Python-%s-HDF5-%s-serial' %(pyver, hdf5ver) - -dependencies = [ - ('Python', pyver), - ('h5py', '2.5.0', versionsuffix), - ('molmod', '1.1', '-Python-%s' %(pyver)), -] - -options = {'modulename': name} -#runtest = 'python setup.py build_ext -i; nosetests -v' - - -pyshortver = ".".join(pyver.split(".")[:-1]) -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver, name)] -} - -moduleclass = 'chem' -- GitLab From 64f041f458140135cc968ab38b501f064d5b48ab Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 14:06:57 +0100 Subject: [PATCH 149/722] Update eb file to new yaff version with fixed nose tests --- ...Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb new file mode 100644 index 0000000000..235257521b --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'yaff' +version = '1.0.develop.2.14' + +homepage = 'http://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.10' + +hdf5ver = '1.8.15-patch1' +versionsuffix = '-Python-%s-HDF5-%s-serial' %(pyver, hdf5ver) + +dependencies = [ + ('Python', pyver), + ('h5py', '2.5.0', versionsuffix), + ('molmod', '1.1', '-Python-%s' %(pyver)), +] + +options = {'modulename': name} +runtest = 'python setup.py build_ext -i; nosetests -v' + + +pyshortver = ".".join(pyver.split(".")[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver, name)] +} + +moduleclass = 'chem' -- GitLab From 91129f8059eb0c9f1fa4fa0dc74b8ea1d0fb46c8 Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 14:10:49 +0100 Subject: [PATCH 150/722] Update QuickFF eb file to new yaff version --- .../q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb index 5d737222c9..8eea2d3e11 100644 --- a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb @@ -23,7 +23,7 @@ dependencies = [ (python, pythonversion), ('matplotlib', '1.5.0', versionsuffix), ('molmod', '1.1', versionsuffix), - ('yaff', '1.0.develop.2.13', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) + ('yaff', '1.0.develop.2.14', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) ] sanity_check_paths = { -- GitLab From ac747bc3fc479757aa6d8eee896e4afab6afbb07 Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 16:28:10 +0100 Subject: [PATCH 151/722] Add eb file to build the molmod dependency of yaff and QuickFF --- .../molmod-1.1-intel-2015b-Python-2.7.10.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..c36da2b123 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0 on 2015-10-01_15-35-44 +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.1' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.5.0', versionsuffix), +] + +options = {'modulename': 'molmod'} +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion] +} + +moduleclass = 'math' -- GitLab From 9cb1e88ea4838c9df0b08239be240363570cdbce Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 15 Mar 2016 16:47:53 +0100 Subject: [PATCH 152/722] added segemehl-0.2.0-goolf-1.4.10.eb --- .../s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..39c950b357 --- /dev/null +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = "segemehl" +version = "0.2.0" + +homepage = 'http://www.bioinf.uni-leipzig.de/Software/segemehl/' +description = """ segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping + and split read mapping. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/'] +sources = ['%s_%s.tar.gz' % (name, version.replace('.','_'))] + +parallel = 1 + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +files_to_copy = [(["lack.x", "segemehl.x", "testrealign.x"], "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["lack.x" , "segemehl.x", "testrealign.x"]], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From c6064624c6bb7e484e21937dab0998fe75398bd4 Mon Sep 17 00:00:00 2001 From: Louis Vanduyfhuys Date: Tue, 15 Mar 2016 19:05:38 +0100 Subject: [PATCH 153/722] Fix matplotlib bug in yaff eb --- ....2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb index 235257521b..29a3cca013 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -23,7 +23,7 @@ dependencies = [ ] options = {'modulename': name} -runtest = 'python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' pyshortver = ".".join(pyver.split(".")[:-1]) -- GitLab From 914b6e8207bd07567fb6c7b86c037e9ed21862fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 22:45:23 +0100 Subject: [PATCH 154/722] style fixes --- .../molmod-1.1-intel-2015b-Python-2.7.10.eb | 18 ++++++----------- ...QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb | 15 +++++--------- ...Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 20 ++++++++----------- 3 files changed, 19 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb index c36da2b123..4fd3ed9a53 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb @@ -1,8 +1,8 @@ -# Built with EasyBuild version 2.2.0 on 2015-10-01_15-35-44 -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'molmod' version = '1.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" @@ -12,23 +12,17 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/molmod/molmod/releases/download/v%(version)s'] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.10' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - dependencies = [ - (python, pythonversion), + ('Python', '2.7.10'), ('matplotlib', '1.5.0', versionsuffix), ] -options = {'modulename': 'molmod'} -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion] + 'dirs': ['lib/python%(pyshortver)s/site-packages/molmod'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb index 8eea2d3e11..1920995e1b 100644 --- a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.0.1-intel-2015b-Python-2.7.10.eb @@ -1,7 +1,8 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'QuickFF' version = '2.0.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/QuickFF/' description = """QuickFF is a Python package developed at the Center for @@ -13,22 +14,16 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/molmod/QuickFF/releases/download/v%(version)s'] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.10' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - dependencies = [ - (python, pythonversion), + ('Python', '2.7.10'), ('matplotlib', '1.5.0', versionsuffix), ('molmod', '1.1', versionsuffix), - ('yaff', '1.0.develop.2.14', '%s-HDF5-1.8.15-patch1-serial' %(versionsuffix)) + ('yaff', '1.0.develop.2.14', '%s-HDF5-1.8.15-patch1-serial' % versionsuffix), ] sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb index 29a3cca013..8d4f8961ee 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -1,7 +1,9 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'yaff' version = '1.0.develop.2.14' +hdf5ver = '1.8.15-patch1' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s-serial' % hdf5ver homepage = 'http://molmod.github.io/yaff/' description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" @@ -11,25 +13,19 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -pyver = '2.7.10' - -hdf5ver = '1.8.15-patch1' -versionsuffix = '-Python-%s-HDF5-%s-serial' %(pyver, hdf5ver) - dependencies = [ - ('Python', pyver), + ('Python', '2.7.10'), ('h5py', '2.5.0', versionsuffix), - ('molmod', '1.1', '-Python-%s' %(pyver)), + ('molmod', '1.1', '-Python-%(pyver)s'), ] options = {'modulename': name} -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' - +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" -pyshortver = ".".join(pyver.split(".")[:-1]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver, name)] + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], } moduleclass = 'chem' -- GitLab From e67988bafa0f2ee3059dc1d3611aabf40343ff48 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 10:00:06 +0200 Subject: [PATCH 155/722] Contributing Python package CosmoloPy --- ...oloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..61bd20053b --- /dev/null +++ b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'CosmoloPy' +version = '0.1.104' + +homepage = 'https://github.com/roban/CosmoloPy' +description = """A cosmology package for Python. CosmoloPy is +built on and designed for use with NumPy and SciPy.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('numpy', '1.7.1', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' -- GitLab From 73c4c8939f69bd0fbb50a0a028c6205dd963ec1f Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 10:34:47 +0200 Subject: [PATCH 156/722] Contributing Python package astropy --- ...astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..bab7a31bcf --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'astropy' +version = '1.0.6' + +homepage = 'http://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('setuptools', '18.4', versionsuffix), + ('numpy', '1.7.1', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' -- GitLab From 58f33889facc9683c075bd35e88b4001ca178c81 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 10:36:10 +0200 Subject: [PATCH 157/722] Contriburing Python package Whoosh --- .../Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..db2dcb5741 --- /dev/null +++ b/easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'Whoosh' +version = '2.7.0' + +homepage = 'https://pypi.python.org/pypi/Whoosh/' +description = """Fast, pure-Python full text indexing, +search, and spell checking library.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pyver = '2.7.3' +pyshortver = ".".join(pyver.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), + ('numpy','1.6.2', versionsuffix), + ('scipy', '0.11.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'lib' -- GitLab From ff336d5b553615453f6611f73f2be8e247eba528 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 12:29:49 +0200 Subject: [PATCH 158/722] Adding setuptools config --- ...oloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb | 31 ------------------- ...tuptools-18.4-goolf-1.4.10-Python-2.7.3.eb | 29 +++++++++++++++++ 2 files changed, 29 insertions(+), 31 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb deleted file mode 100644 index 61bd20053b..0000000000 --- a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = "PythonPackage" - -name = 'CosmoloPy' -version = '0.1.104' - -homepage = 'https://github.com/roban/CosmoloPy' -description = """A cosmology package for Python. CosmoloPy is -built on and designed for use with NumPy and SciPy.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -python = 'Python' -pyver = '2.7.3' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('numpy', '1.7.1', versionsuffix), -] - -pyshortver = '.'.join(pyver.split('.')[:2]) - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..e4b06a51e1 --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = "setuptools" +version = "18.4" + +homepage = "http://pypi.python.org/pypi/setuptools/" +description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.3" + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +py_short_ver = ".".join(pythonversion.split(".")[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], + 'dirs': [] + } + +moduleclass = 'devel' -- GitLab From 06e9ae546aa45bcdec0db8857ed5e251dfbd9e2a Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 12:34:27 +0200 Subject: [PATCH 159/722] Updated PR, deleted unwanted files --- ...astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb | 33 ------------------- ...oloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb | 31 ----------------- 2 files changed, 64 deletions(-) delete mode 100644 easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb delete mode 100644 easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb deleted file mode 100644 index bab7a31bcf..0000000000 --- a/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = "PythonPackage" - -name = 'astropy' -version = '1.0.6' - -homepage = 'http://www.astropy.org/' -description = """The Astropy Project is a community effort to develop -a single core package for Astronomy in Python and foster interoperability -between Python astronomy packages.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -python = 'Python' -pyver = '2.7.3' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('setuptools', '18.4', versionsuffix), - ('numpy', '1.7.1', versionsuffix), -] - -pyshortver = '.'.join(pyver.split('.')[:2]) - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb deleted file mode 100644 index 61bd20053b..0000000000 --- a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = "PythonPackage" - -name = 'CosmoloPy' -version = '0.1.104' - -homepage = 'https://github.com/roban/CosmoloPy' -description = """A cosmology package for Python. CosmoloPy is -built on and designed for use with NumPy and SciPy.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -python = 'Python' -pyver = '2.7.3' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('numpy', '1.7.1', versionsuffix), -] - -pyshortver = '.'.join(pyver.split('.')[:2]) - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'tools' -- GitLab From 43d5d37b7ce6fea2f8c9ef312f9543b99a245175 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Wed, 16 Mar 2016 12:40:08 +0100 Subject: [PATCH 160/722] Fix typo --- easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb index 391d1f7f0c..d81b50276d 100644 --- a/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb +++ b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb @@ -26,7 +26,7 @@ comp_mpi_tc = (comp_mpi_tc_name, version) # For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ ('GCC', gccver), - ('MVAPICH2', '2.2b', '', ('GCC', gccver)), + ('MPICH', '3.2', '', ('GCC', gccver)), (blaslib, blasver, blassuff, ('GCC', gccver)), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), -- GitLab From 82a53a3c9515ca386991a88206c2d6f51549e672 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Wed, 16 Mar 2016 12:40:22 +0100 Subject: [PATCH 161/722] Cleanup --- easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb | 5 +---- easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb | 5 +---- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb index d495830401..45cf27aa8b 100644 --- a/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb +++ b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb @@ -13,13 +13,10 @@ compname = 'GCC' compver = '4.9.3-2.25' comp = (compname, compver) -mpilib = 'MPICH' -mpiver = '3.2' - # compiler toolchain dependencies dependencies = [ comp, - (mpilib, mpiver, '', comp), + ('MPICH', '3.2', '', comp), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb index efd6351300..80a9588d01 100644 --- a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb +++ b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb @@ -13,13 +13,10 @@ compname = 'GCC' compver = '4.9.3-2.25' comp = (compname, compver) -mpilib = 'MVAPICH2' -mpiver = '2.2b' - # compiler toolchain dependencies dependencies = [ comp, - (mpilib, mpiver, '', comp), + ('MVAPICH2', '2.2b', '', comp), ] moduleclass = 'toolchain' -- GitLab From dff5ae0ec1e64be935bb7cb8270f1fa2b67eeeb3 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Wed, 16 Mar 2016 12:43:53 +0100 Subject: [PATCH 162/722] Add easyconfig for HPL with the two new toolchain gmpolf/2016a and gmvpolf/2016a --- .../easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb | 18 ++++++++++++++++++ .../easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb new file mode 100644 index 0000000000..ae8a971cbf --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gmpolf', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb new file mode 100644 index 0000000000..d581afc6f7 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gmvolf', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From a8ab9324ac69573f4d59b9a6242c17dbe2a39137 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Mar 2016 14:15:18 +0200 Subject: [PATCH 163/722] Fixing indent --- .../setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb index e4b06a51e1..0b0cd4ff22 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-18.4-goolf-1.4.10-Python-2.7.3.eb @@ -22,8 +22,8 @@ py_short_ver = ".".join(pythonversion.split(".")[0:2]) pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) sanity_check_paths = { - 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], - 'dirs': [] - } + 'files': ["bin/easy_install", "%s-%s-py%s.egg" % (pylibdir, version, py_short_ver)], + 'dirs': [] +} moduleclass = 'devel' -- GitLab From 4f13a60ee4d93dc68fb5a87bd68698ec5c406b6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 15:03:14 +0100 Subject: [PATCH 164/722] add postinstall command to fix permission issues in molmod easyconfig file --- .../m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb index 4fd3ed9a53..ee1c589750 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb @@ -20,6 +20,9 @@ dependencies = [ runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" runtest += "python setup.py build_ext -i; nosetests -v" +# fix permissions issue on files in share/molmod subdir +postinstallcmds = ['chmod -R o+r %(installdir)s/share/molmod'] + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/molmod'], -- GitLab From 38320cfa41dcfd4886d5f64b5c19244705106374 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 16:14:22 +0100 Subject: [PATCH 165/722] Revert "Updated PR, deleted unwanted files" This reverts commit 06e9ae546aa45bcdec0db8857ed5e251dfbd9e2a. --- ...astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb | 33 +++++++++++++++++++ ...oloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb | 31 +++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..bab7a31bcf --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-1.0.6-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'astropy' +version = '1.0.6' + +homepage = 'http://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('setuptools', '18.4', versionsuffix), + ('numpy', '1.7.1', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..61bd20053b --- /dev/null +++ b/easybuild/easyconfigs/c/CosmoloPy/CosmoloPy-0.1.104-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'CosmoloPy' +version = '0.1.104' + +homepage = 'https://github.com/roban/CosmoloPy' +description = """A cosmology package for Python. CosmoloPy is +built on and designed for use with NumPy and SciPy.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('numpy', '1.7.1', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' -- GitLab From 1a564ebd3f7b674fc01c16277f53d0ba79399ff2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 17:45:23 +0200 Subject: [PATCH 166/722] add easyconfig PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb --- .../PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyAMG/PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..25956cf16e --- /dev/null +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-3.0.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'PyAMG' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pyamg.org' +description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +options = {'modulename': 'pyamg'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pyamg'], +} + +moduleclass = 'math' -- GitLab From df381842df1ab423a230a44afd0921ec33e2f3d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 18:39:27 +0100 Subject: [PATCH 167/722] reinstate Velvet easyconfigs that were removed in #2495 --- .../Velvet-1.2.10-intel-2015b-mt-kmer_100.eb | 29 ++++++++++++++++++ .../Velvet-1.2.10-intel-2015b-mt-kmer_31.eb | 30 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb create mode 100644 easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb new file mode 100644 index 0000000000..70b05647b0 --- /dev/null +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute +# Authors:: Cedric Laczny , Fotis Georgatos , +# Thekla Loizou , Andreas Panteli +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Velvet' +version = '1.2.10' +versionsuffix = '-mt-kmer_100' + +homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +description = """Sequence assembler for very short reads""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} + +sources = ['%(namelower)s_%(version)s.tgz'] +source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] + +buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb new file mode 100644 index 0000000000..fff6a988ab --- /dev/null +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute +# Authors:: Cedric Laczny , Fotis Georgatos , +# Thekla Loizou , Andreas Panteli +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Velvet' +version = '1.2.10' +versionsuffix = '-mt-kmer_31' + +homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +description = """Sequence assembler for very short reads""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} + +sources = ['%(namelower)s_%(version)s.tgz'] +source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] + +# by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous +buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] + +moduleclass = 'bio' -- GitLab From 90fa22472b6cfc099996ca3b9335d92339d1041e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 16 Mar 2016 18:45:42 +0100 Subject: [PATCH 168/722] rainbow-2.0.4-goolf-1.4.10.eb --- .../r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..c431cc2a4f --- /dev/null +++ b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'rainbow' +version = '2.0.4' + +homepage = 'https://sourceforge.net/projects/bio-rainbow/' +description = """Efficient tool for clustering and assembling short reads, especially for RAD.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://downloads.sourceforge.net/project/bio-rainbow/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +buildopts = ' CC=$CC' + +files_to_copy = [(['rainbow', 'ezmsim', 'rbasm', 'select_sec_rbcontig.pl', + 'select_best_rbcontig_plus_read1.pl', 'select_sec_rbcontig.pl', 'select_all_rbcontig.pl'], 'bin')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/rainbow', 'bin/ezmsim', 'bin/rbasm'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 7e1d2ba87aabccafdc34a72438f79de067394201 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 16 Mar 2016 18:47:49 +0100 Subject: [PATCH 169/722] PEAR-0.9.6-goolf-1.4.10.eb --- .../p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb new file mode 100644 index 0000000000..5ee2eb89d1 --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.6' + +homepage = 'http://sco.h-its.org/exelixis/web/software/pear/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sco.h-its.org/exelixis/web/software/pear/files/'] +sources = ['%(namelower)s-%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/pear'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 0e5d1dc188f3920467c8ddd6ff17c9fd7ac64b5c Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 16 Mar 2016 18:50:52 +0100 Subject: [PATCH 170/722] Mawk-1.3.4-goolf-1.4.10-20150503.eb --- .../Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb diff --git a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb new file mode 100644 index 0000000000..7235621e5d --- /dev/null +++ b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'Mawk' +version = '1.3.4' +versionsuffix = '-20150503' + +homepage = 'http://invisible-island.net/mawk/' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['ftp://invisible-island.net/mawk/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 8ac95fa17358dc9aa92a48df101ea2a2074e3dae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 20:30:58 +0100 Subject: [PATCH 171/722] reinstate building MetaVelvet and copying contrib in Velvet easyconfigs --- .../v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb | 2 ++ .../v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb index 70b05647b0..52c0ab85db 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb @@ -26,4 +26,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb index fff6a988ab..c23584dddd 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb @@ -27,4 +27,6 @@ source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] # by default MAXKMERLENGTH=31 but defined here to keep all the easyconfigs homogeneous buildopts = "OPENMP=1 MAXKMERLENGTH=%s" % versionsuffix.split('_')[1] +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] + moduleclass = 'bio' -- GitLab From 97559c46c82ca98f9214ed35f1ba78d4349a81ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2016 20:55:24 +0100 Subject: [PATCH 172/722] bump version to 2.7.0 and update release notes --- RELEASE_NOTES | 73 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 73 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a3e8287af7..b2548fe550 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,80 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 5,093 easyconfig files, for 799 different software packages, +The latest version of easybuild-easyconfig provides 5,580 easyconfig files, for 862 different software packages, 34 different (compiler) toolchains, 12 software bundles and 1 meta-package. +v2.7.0 (March 18th 2016) +------------------------ + +feature + bugfix release +- added example easyconfig files for 63 new software packages: + ATSAS (#616, #2587), astropy (#2724, #2727), attr (#2706), BamUtil (#2654), BBMap (#2322), BH (#2508), + CheMPS2 (#2445), CosmoloPy (#2723, #2727), csvkit (#2639), Firefox (#2648), FreeXL (#2422), GL2PS (#2667), + Glade (#2631), htop (#2538), IGV (#2019), IGVTools (#2019), ImageMagick (#2438), jModelTest (#2529), + KEALib (#2420), libcerf (#2656), libgcrypt (#2201), libglade (#2631), libgpg-error (#2201), libspatialite (#2431), + LittleCMS (#2438), MAST (#2542), MLC (#2577), MPJ-Express (#2529), mutil (#2201), neon (#758), NextClip (#2544), + npstat (#2686, #2703), Octopus (#2643), QuickFF (#2721), p4vasp (#2328), PCMSolver (#2445), PFFT (#2643), + PHYLIP (#2694), pkgconfig (#2475, #2476), Platypus (#2618), pplacer (#1056), PRINSEQ (#2437, #2444, #2585), + PyFFmpeg (#2501, #2519), PyGObject (#2443), PyGTK (#2443), PyOpenGL (#2628), pyringe (#2533), qrupdate (#2675), + rgeos (#2635), rpmrebuild (#2402), shift (#2201), SNAPE-pooled (#2688), SNPhylo (#2701), sratoolkit (#2715), + STAR-Fusion (#2463), statsmodels (#2719), StringTie (#2527), synchronicity (#2508), testpath (#2461), + USEARCH (#2537), VarScan (#2464), vsc-install (#2165), Whoosh (#2725), xprop (#2645) +- added new easyconfigs for existing toolchains: + intel/2016.02-GCC-4.9 (#2620), gmpolf/2016a & gmvolf/2016a (#2589) +- stable Cray-specific easyconfigs + - delete deprecated Cray toolchains and easyconfig files (#2400) + - don't hardcode PrgEnv version, remove craype and fftw components in Cray toolchains (#2554) + - remove -XC versionsuffix for stable definitions for Cray* toolchains (#2714) + - support for various software packages with CrayGNU and CrayIntel toolchains: CP2K, GROMACS, WRF +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including BWA 0.7.13, CMake 3.4.3, GATE 7.2, GROMACS 5.1.2, Mesa 11.1.2, netCDF 4.4.0, Perl 5.22.1, Python 3.5.1, + R 3.2.3, R-bundle-Bioconductor 3.2, scipy 0.17.0, SuiteSparse 4.5.1 +- various other enhancements, including: + - copy contrib dir in Velvet easyconfigs so scripts are also available (#2456) + - redefine matplotlib 1.5.1 easyconfig as a bundle, also include cycler extension (dep for matplotlib) (#2470) + - add bitstring extension to Python 2.7.11 easyconfigs (#2471) + - enable building of MetaVelvet in Velvet 1.2.10 easyconfigs (#2473) + - add custom sanity check for libjpeg-turbo (#2480) + - add Velvet easyconfigs that include BioPerl dependency, so VelvetOptimizer can use it (#2495, #2729, #2733) + - add source URL in RAxML 7.2.6 easyconfigs (#2536) + - update MPICH easyconfigs to use new MPICH easyblock (#2589) + - free libX11 & co from unneeded Python dependency/versionsuffix (#2549, #2563, #2605, #2664) + - add '--enable-utf --enable-unicode-properties' configure options in PCRE easyconfigs (#2561) + - required for latest R versions + - add HCsnip, metagenomeSeq in Bioconductor 3.1 bundles (#2553, #2578) + - add additional extensions in R 3.2.x easyconfigs that are required for extra Bioconductor extensions (#2547, #2556) + - update psmpi easyconfig files to use the new psmpi easyblock (#2619) + - add easyconfig for Python 2.7.11 on top of X11-enabled Tk (#2614, #2621) + - add virtualenv as extension in Python 2.7.11 easyconfigs (#2660) +- various bug fixes, including: + - fix software name for GTK+ (was 'gtk+'), PyCairo (was 'pycairo') and Gdk-Pixbuf (was 'gdk-pixbuf') (#2468) + - don't hardcode CC/CXX in OpenMPI easyconfigs (#2472) + - remove Google Code source URL for mpi4py (#2474) + - rename ffmpeg to FFmpeg (#2425, #2481) + - use available easyblock for flex (#2486) + - fix determining list of easyconfigs in unit test suite, don't assume locations are correct (#2530) + - fix specifying DB dependency in DB_File easyconfigs (#2539) + - remove hard-coded -xSSE4.2 for numpy/scipy with Intel compilers (#2546) + - fix license headers: Hercules foundation is now FWO (#2550) + - add --with-zlib configure argument in libxml easyconfigs (#2555) + - don't hardcode optarch=True in xextproto/xtrans easyconfigs (#2601) + - change toolchain version to '' in easyconfigs that use dummy toolchain and include dependencies (#2612) + - GLib doesn't require libxml2 with Python bindings (#2632) + - add patch file to imkl 10.2.6.038 32-bit easyconfig to fix installer not being able to deal with '--' in build path (#2634) + - add missing 'pkgconfig' dependency for h5py (#2476, #2650) + - correct software name in FastQC easyconfigs (was 'fastqc'), use 'dummy' toolchain for all FastQC version (#2657, #2666) + - add missing libxml2 dependencies in GLib easyconfigs (#2658) + - fix Xerces-C++ download location (#2668) + - enable XML::Bare extension in all Perl easyconfigs (#2672) + - update dead link for SuiteSparse (#2679) + - remove custom exts_filter in easyconfigs used PythonPackage easyblock (#2683, #2685) + - add M4 as build dep for binutils & flex (#2681) + - add missing dependencies in Python 3.5.x easyconfigs: SQLite, Tk, GMP (#2704) + - fix (OS) deps, add checksums, remove parameter definition with default values in MVAPICH2 easyconfigs (#2707) +- style cleanup in various easyconfigs (#2378, #2387, #2395, #2396, #2488-#2493, #2496-#2500, #2502-#2504, #2602) + - working towards automated style review of pull requests + v2.6.0 (January 26th 2016) -------------------------- diff --git a/setup.py b/setup.py index e1abe096bf..bbfef2ebfa 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.7.0.dev0' +VERSION = '2.7.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 887023130eadcc6a55f01d695d6cec31ef56a599 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 17 Mar 2016 14:17:05 -0500 Subject: [PATCH 173/722] Adding an Easyconfig file for gtool-v0.7.5 --- .../g/gtool/gtool-0.7.5_linux_x86_64.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb new file mode 100644 index 0000000000..276283587b --- /dev/null +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: + +easyblock = "Binary" + +name = 'gtool' +version = '0.7.5' +versionsuffix = '_linux_x86_64' + +homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' +description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] +sources = ['gtool_v%(version)s_x86_64.tgz'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["gtool", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' -- GitLab From 02c80db3e5edf4c515e7c2e84cba772f41ed4867 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 17 Mar 2016 16:55:18 -0500 Subject: [PATCH 174/722] Adding Easyconfig file for shapeit_v2.r837_GLIBCv2.12 --- ...shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb diff --git a/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb new file mode 100644 index 0000000000..a71ba8d96d --- /dev/null +++ b/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi + +easyblock = "Binary" + +name = 'shapeit' +version = '2.r837.GLIBCv2.12' +versionsuffix = '_linux_x86_64' + +homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html' +description = """ SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] +sources = ['shapeit.v%(version)s.Linux.static.tgz'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "tar xzvf shapeit.v%(version)s.Linux.static.tgz && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["bin/shapeit", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' -- GitLab From 4ac34ac670957972ae454538b960cf7b2b57bd5e Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 17 Mar 2016 17:08:51 -0500 Subject: [PATCH 175/722] Adding author to the Easyconfig file for gtool --- easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb index 276283587b..aa280fb576 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -1,5 +1,5 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: +# Author: Ravi Tripathi easyblock = "Binary" -- GitLab From b42b09ef2b1fdebe5b1d98891eed75169834e0f9 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 18 Mar 2016 02:12:56 -0500 Subject: [PATCH 176/722] Changing the name of Easyconfig file for gtool v0.7.5 --- .../g/gtool/gtool-0.7.5-linux_x86_64.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb new file mode 100644 index 0000000000..aa280fb576 --- /dev/null +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi + +easyblock = "Binary" + +name = 'gtool' +version = '0.7.5' +versionsuffix = '_linux_x86_64' + +homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' +description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] +sources = ['gtool_v%(version)s_x86_64.tgz'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["gtool", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' -- GitLab From 38474722b49c807cdbe36716e92088c8f989803d Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 18 Mar 2016 02:15:47 -0500 Subject: [PATCH 177/722] Changing the name of Easyconfig file for gtool v0.7.5 --- .../g/gtool/gtool-0.7.5_linux_x86_64.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb deleted file mode 100644 index aa280fb576..0000000000 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ /dev/null @@ -1,27 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Ravi Tripathi - -easyblock = "Binary" - -name = 'gtool' -version = '0.7.5' -versionsuffix = '_linux_x86_64' - -homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' -description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] -sources = ['gtool_v%(version)s_x86_64.tgz'] - -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " -install_cmd += "cp -a %(builddir)s/* %(installdir)s" - -sanity_check_paths = { - 'files': ["gtool", "LICENCE"], - 'dirs': ["example"] -} - -moduleclass = 'bio' -- GitLab From 9f51538585027769015932d76f80f27967b610f7 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 18 Mar 2016 02:19:51 -0500 Subject: [PATCH 178/722] Change the name of easyconfig file for shapeit-v2.r837_GLIBCv2.12 --- ...linux_x86_64.eb => shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/shapeit/{shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb => shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb} (100%) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb rename to easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb -- GitLab From 73c1f0a92e6ba69c9a6e6b0aaee1edc1ec9a395a Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Fri, 18 Mar 2016 10:39:18 -0400 Subject: [PATCH 179/722] Add easyconfig BWA-0.7.13-goolf-1.4.10 --- .../b/BWA/BWA-0.7.13-goolf-1.4.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb new file mode 100644 index 0000000000..403c2a7c2e --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos , Daniel Navarro +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'BWA' +version = '0.7.13' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] + +moduleclass = 'bio' -- GitLab From 808d1eb56e319ed017b07fb3b2e748acb67f7686 Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Fri, 18 Mar 2016 11:03:07 -0400 Subject: [PATCH 180/722] Including zlib as dependency for BWA-0.7.13-goolf-1.4.10.eb --- easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb index 403c2a7c2e..439ab3ce81 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -19,6 +19,7 @@ description = """Burrows-Wheeler Aligner (BWA) is an efficient program that alig toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} +dependencies = [('zlib', '1.2.8')] sources = [SOURCELOWER_TAR_BZ2] source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] -- GitLab From 4e25132c4035aabb3f79d24934f93419d26090b7 Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Fri, 18 Mar 2016 11:07:02 -0400 Subject: [PATCH 181/722] Style fix --- easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb index 439ab3ce81..9cbb01f191 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -19,9 +19,10 @@ description = """Burrows-Wheeler Aligner (BWA) is an efficient program that alig toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -dependencies = [('zlib', '1.2.8')] sources = [SOURCELOWER_TAR_BZ2] source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] +dependencies = [('zlib', '1.2.8')] + moduleclass = 'bio' -- GitLab From 9f856123b6f4837cfafad3e129861c9e1fb14293 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sat, 19 Mar 2016 10:54:21 +0100 Subject: [PATCH 182/722] fixed foss easyconfig --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb index 2ecf3ea45f..67cfd94871 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -153,7 +153,7 @@ exts_list = [ }), ('Archive::Extract', '0.76', { 'source_tmpl': 'Archive-Extract-0.76.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "BINGOS"'], + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS'], }), ('DBIx::Simple', '1.35', { 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', @@ -405,7 +405,7 @@ exts_list = [ }), ('Date::Language', '2.30', { 'source_tmpl': 'TimeDate-2.30.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "GBARR"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], }), ('version', '0.9915', { 'source_tmpl': 'version-0.9915.tar.gz', @@ -546,7 +546,7 @@ exts_list = [ }), ('boolean', '0.45', { 'source_tmpl': 'boolean-0.45.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "INGY"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], }), ('Number::Format', '1.75', { 'source_tmpl': 'Number-Format-1.75.tar.gz', -- GitLab From 3fad4beecd206cdad60adebf2b8719dc3051d37c Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sat, 19 Mar 2016 10:56:24 +0100 Subject: [PATCH 183/722] fixed intel easyconfig --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index ae84220ef2..fd9ccde670 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -153,7 +153,7 @@ exts_list = [ }), ('Archive::Extract', '0.76', { 'source_tmpl': 'Archive-Extract-0.76.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "BINGOS"'], + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS'], }), ('DBIx::Simple', '1.35', { 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', @@ -405,7 +405,7 @@ exts_list = [ }), ('Date::Language', '2.30', { 'source_tmpl': 'TimeDate-2.30.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "GBARR"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], }), ('version', '0.9915', { 'source_tmpl': 'version-0.9915.tar.gz', @@ -547,7 +547,7 @@ exts_list = [ }), ('boolean', '0.45', { 'source_tmpl': 'boolean-0.45.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/ / "/ "INGY"'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], }), ('Number::Format', '1.75', { 'source_tmpl': 'Number-Format-1.75.tar.gz', -- GitLab From 8e71210d0960333d22b625b7fac297dd84f5a7a0 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sat, 19 Mar 2016 12:12:16 +0100 Subject: [PATCH 184/722] updated url --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb index 67cfd94871..404b98df7e 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -153,7 +153,7 @@ exts_list = [ }), ('Archive::Extract', '0.76', { 'source_tmpl': 'Archive-Extract-0.76.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), ('DBIx::Simple', '1.35', { 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index fd9ccde670..aed8a467d0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -153,7 +153,7 @@ exts_list = [ }), ('Archive::Extract', '0.76', { 'source_tmpl': 'Archive-Extract-0.76.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), ('DBIx::Simple', '1.35', { 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', -- GitLab From df78df46c817032519ddcb787df100b0c846983d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 20 Mar 2016 08:50:34 +0100 Subject: [PATCH 185/722] fix release date for EasyBuild v2.7.0 --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b2548fe550..b5c225454e 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,7 +6,7 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 5,580 easyconfig files, for 862 different software packages, 34 different (compiler) toolchains, 12 software bundles and 1 meta-package. -v2.7.0 (March 18th 2016) +v2.7.0 (March 20th 2016) ------------------------ feature + bugfix release -- GitLab From 972a0974247a5f3641728f8fcdce30c47e4b4835 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 20 Mar 2016 10:45:38 +0100 Subject: [PATCH 186/722] bump version to 2.8.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index bbfef2ebfa..72cf85df21 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.7.0' +VERSION = '2.8.0dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From f2ecb8a398d2a16aecb24c378131202077b6f485 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 20 Mar 2016 11:45:55 +0200 Subject: [PATCH 187/722] add easyconfig EasyBuild-2.7.0.eb --- .../e/EasyBuild/EasyBuild-2.7.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb new file mode 100644 index 0000000000..1ca29896e8 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.7.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.4.18.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 4dcdd9aa5726c945a7301332f00b431d1db3da86 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 08:30:39 +0100 Subject: [PATCH 188/722] add easyconfig inputproto-2.3.1-foss-2016a.eb, add easyconfig kbproto-1.0.7-foss-2016a.eb, add easyconfig libpthread-stubs-0.3-foss-2016a.eb, add easyconfig libX11-1.6.3-foss-2016a.eb, add easyconfig libXau-1.0.8-foss-2016a.eb, add easyconfig libxcb-1.11.1-foss-2016a.eb, add easyconfig libXdmcp-1.1.2-foss-2016a.eb, add easyconfig xextproto-7.3.0-foss-2016a.eb, add easyconfig xproto-7.0.28-foss-2016a.eb, add easyconfig xtrans-1.3.5-foss-2016a.eb --- .../inputproto/inputproto-2.3.1-foss-2016a.eb | 19 ++++++++++ .../k/kbproto/kbproto-1.0.7-foss-2016a.eb | 19 ++++++++++ .../l/libX11/libX11-1.6.3-foss-2016a.eb | 37 +++++++++++++++++++ .../l/libXau/libXau-1.0.8-foss-2016a.eb | 25 +++++++++++++ .../l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 25 +++++++++++++ .../libpthread-stubs-0.3-foss-2016a.eb | 20 ++++++++++ .../l/libxcb/libxcb-1.11.1-foss-2016a.eb | 33 +++++++++++++++++ .../x/xextproto/xextproto-7.3.0-foss-2016a.eb | 24 ++++++++++++ .../x/xproto/xproto-7.0.28-foss-2016a.eb | 23 ++++++++++++ .../x/xtrans/xtrans-1.3.5-foss-2016a.eb | 22 +++++++++++ 10 files changed, 247 insertions(+) create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb new file mode 100644 index 0000000000..be4171cde7 --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb new file mode 100644 index 0000000000..bca5ddd7ca --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb new file mode 100644 index 0000000000..7bbdcf2dc4 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..8694ab5ad2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c12e65e6e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb new file mode 100644 index 0000000000..fcb767cfdb --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb new file mode 100644 index 0000000000..d818b47843 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb new file mode 100644 index 0000000000..9bc6335cdf --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb new file mode 100644 index 0000000000..3e787177f0 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb new file mode 100644 index 0000000000..1d32cb1ae6 --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From a07b7c3608e80cb5bbbcd8ad159231b462582047 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 08:39:44 +0100 Subject: [PATCH 189/722] add easyconfig libXext-1.3.3-foss-2016a.eb --- .../l/libXext/libXext-1.3.3-foss-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000..fc57003279 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From ada59b306cff8427daa61380d50f9e4419e1f6dc Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 08:56:07 +0100 Subject: [PATCH 190/722] add easyconfig libXft-2.3.2-foss-2016a.eb, add easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig freetype-2.6.2-foss-2016a.eb, add easyconfig libXrender-0.9.9-foss-2016a.eb, add easyconfig renderproto-0.11-foss-2016a.eb --- .../fontconfig-2.11.94-foss-2016a.eb | 22 +++++++++++++ .../f/freetype/freetype-2.6.2-foss-2016a.eb | 22 +++++++++++++ .../l/libXft/libXft-2.3.2-foss-2016a.eb | 31 +++++++++++++++++++ .../libXrender/libXrender-0.9.9-foss-2016a.eb | 28 +++++++++++++++++ .../renderproto-0.11-foss-2016a.eb | 20 ++++++++++++ 5 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb new file mode 100644 index 0000000000..d955835431 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.94' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.6.2'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb new file mode 100644 index 0000000000..41c2f0204e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb new file mode 100644 index 0000000000..1a968a5ada --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXrender', '0.9.9'), + ('freetype', '2.6.2'), + ('fontconfig', '2.11.94'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb new file mode 100644 index 0000000000..eee347a314 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb new file mode 100644 index 0000000000..48199d0511 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 61e73501ae42f1a56e50031555bd20d3cf4aeb0d Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 09:00:48 +0100 Subject: [PATCH 191/722] add easyconfig PCRE-8.38-foss-2016a.eb --- .../p/PCRE/PCRE-8.38-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb new file mode 100644 index 0000000000..1fe2fcb26c --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.38' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' -- GitLab From d84ea63b7582b3cf1d54b1bc07bdc32a2da5222c Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Mon, 21 Mar 2016 17:30:01 +0100 Subject: [PATCH 192/722] New TAMkin easyconfig --- .../TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..9f28a619eb --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'TAMkin' +version = '1.0.8' + +homepage = 'http://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.5.0', versionsuffix), + ('molmod', '1.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion], +} + +moduleclass = 'chem' -- GitLab From 85471cb0716f38691dff6baf1aa00a73ba0845b8 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 17:49:48 +0100 Subject: [PATCH 193/722] add easyconfig gperf-3.0.4-foss-2016a.eb --- .../g/gperf/gperf-3.0.4-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb new file mode 100644 index 0000000000..0547875020 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 1017f5824cdac5303667b828d4b0c54a1b5d73eb Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 18:10:54 +0100 Subject: [PATCH 194/722] modify easyconfig bzip2-1.0.6-foss-2016a.eb, add easyconfig gettext-0.19.6-foss-2016a.eb, add easyconfig GraphicsMagick-1.3.23-foss-2016a.eb, modify easyconfig libjpeg-turbo-1.4.2-foss-2016a.eb, add easyconfig LibTIFF-4.0.6-foss-2016a.eb, modify easyconfig libtool-2.4.6-foss-2016a.eb, modify easyconfig libxml2-2.9.3-foss-2016a.eb, add easyconfig XZ-5.2.2-foss-2016a.eb --- .../GraphicsMagick-1.3.23-foss-2016a.eb | 34 +++++++++++++++++++ .../g/gettext/gettext-0.19.6-foss-2016a.eb | 18 ++++++++++ .../l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb | 33 ++++++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb | 30 ++++++++++++++++ 4 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb new file mode 100644 index 0000000000..e3433e3f0b --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.23' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('libtool', '2.4.6'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('bzip2', '1.0.6'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libxml2', '2.9.3'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb new file mode 100644 index 0000000000..1fdb744032 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.6' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb new file mode 100644 index 0000000000..d7aa3b2df4 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.6' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb new file mode 100644 index 0000000000..2a89ca6af6 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('gettext', '0.19.6'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From e5236a98d2ea36fb4c3a4aa8ed4eb98f0f43f076 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 18:29:11 +0100 Subject: [PATCH 195/722] add easyconfig qrupdate-1.1.2-foss-2016a.eb --- .../q/qrupdate/qrupdate-1.1.2-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..27976f981b --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['%(name)s-%(version)s_makeconf.patch'] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 994d6f447d81fb081150ce1a1aec518a4bd2d45b Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 18:40:00 +0100 Subject: [PATCH 196/722] add easyconfig HDF5-1.8.16-foss-2016a-serial.eb --- .../h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb new file mode 100644 index 0000000000..2936e9795e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.16' +versionsuffix = '-serial' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From 7a94c71bd384f3f1dc82777fc7abd5c24f5fcfab Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 20:51:41 +0100 Subject: [PATCH 197/722] add easyconfig GLib-2.47.5-foss-2016a.eb, add easyconfig libffi-3.2.1-foss-2016a.eb, add easyconfig libICE-1.0.9-foss-2016a.eb, add easyconfig libSM-1.2.2-foss-2016a.eb, add easyconfig libXt-1.1.5-foss-2016a.eb, add easyconfig Qt-4.8.7-foss-2016a.eb --- .../g/GLib/GLib-2.47.5-foss-2016a.eb | 33 ++++++++++++++++ .../l/libICE/libICE-1.0.9-foss-2016a.eb | 27 +++++++++++++ .../l/libSM/libSM-1.2.2-foss-2016a.eb | 28 +++++++++++++ .../l/libXt/libXt-1.1.5-foss-2016a.eb | 39 +++++++++++++++++++ .../l/libffi/libffi-3.2.1-foss-2016a.eb | 23 +++++++++++ .../easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb | 24 ++++++++++++ 6 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb new file mode 100644 index 0000000000..06841954c4 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb new file mode 100644 index 0000000000..fa49f6c97c --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libICE' +version = '1.0.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xtrans', '1.3.5'), +] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb new file mode 100644 index 0000000000..fe3df1bbcf --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libSM' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Session Management library, which allows for applications to both manage sessions, + and make use of session managers to save and restore their state for later use.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libICE', '1.0.9'), +] +builddependencies = [ + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb new file mode 100644 index 0000000000..e37e36b1f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'libXt' +version = '1.1.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are + based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('kbproto', '1.0.7'), +] + +dependencies = [ + ('libSM', '1.2.2'), + ('libICE', '1.0.9'), + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', + 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', + 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', + 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', + 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb new file mode 100644 index 0000000000..c7c638b6fa --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb new file mode 100644 index 0000000000..fd0d5932c9 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb @@ -0,0 +1,24 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +dependencies = [ + ('GLib', '2.47.5'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXrender', '0.9.9'), +] + +moduleclass = 'devel' -- GitLab From 27b9000a75e68f57f624ad38be815faa1baeb57f Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Mon, 21 Mar 2016 21:45:37 +0100 Subject: [PATCH 198/722] Simplify python dependency info in TAMkin easyconfig --- .../t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb index 9f28a619eb..808f61dc12 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb @@ -13,14 +13,10 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/molmod/tamkin/releases/download/v%(version)s'] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.10' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-Python-%(pyver)s" dependencies = [ - (python, pythonversion), + ('Python', '2.7.10'), ('matplotlib', '1.5.0', versionsuffix), ('molmod', '1.1', versionsuffix), ] -- GitLab From 27c1ecfe7002a2e31f8b1719dfd7ee9f8cfa0a41 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Mon, 21 Mar 2016 21:47:46 +0100 Subject: [PATCH 199/722] Move line in TAMkin easyconfig --- .../t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb index 808f61dc12..b5bff455c0 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb @@ -2,6 +2,7 @@ easyblock = "PythonPackage" name = 'TAMkin' version = '1.0.8' +versionsuffix = "-Python-%(pyver)s" homepage = 'http://molmod.github.io/tamkin/' description = """TAMkin is a post-processing toolkit for normal mode analysis, @@ -13,8 +14,6 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/molmod/tamkin/releases/download/v%(version)s'] sources = [SOURCE_TAR_GZ] -versionsuffix = "-Python-%(pyver)s" - dependencies = [ ('Python', '2.7.10'), ('matplotlib', '1.5.0', versionsuffix), -- GitLab From 916e9d74d7e679b04d4ac0e44f1f3df12ca03d13 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:23:46 +0100 Subject: [PATCH 200/722] add easyconfig eudev-3.1.5-foss-2016a.eb, add easyconfig fixesproto-5.0-foss-2016a.eb, add easyconfig fontsproto-2.1.3-foss-2016a.eb, add easyconfig glproto-1.4.17-foss-2016a.eb, add easyconfig libdrm-2.4.67-foss-2016a.eb, add easyconfig libfontenc-1.1.3-foss-2016a.eb, add easyconfig libpciaccess-0.13.4-foss-2016a.eb, add easyconfig libXdamage-1.1.4-foss-2016a.eb, add easyconfig libXfixes-5.0.1-foss-2016a.eb, add easyconfig libXfont-1.5.1-foss-2016a.eb, add easyconfig makedepend-1.0.5-foss-2016a.eb, add easyconfig Mesa-11.1.2-foss-2016a.eb, add easyconfig pkg-config-0.29-foss-2016a.eb, add easyconfig xorg-macros-1.19.0-foss-2016a.eb --- .../e/eudev/eudev-3.1.5-foss-2016a.eb | 32 +++++++++ .../f/fixesproto/fixesproto-5.0-foss-2016a.eb | 19 ++++++ .../fontsproto/fontsproto-2.1.3-foss-2016a.eb | 20 ++++++ .../g/glproto/glproto-1.4.17-foss-2016a.eb | 20 ++++++ .../libXdamage/libXdamage-1.1.4-foss-2016a.eb | 25 +++++++ .../l/libXfixes/libXfixes-5.0.1-foss-2016a.eb | 24 +++++++ .../l/libXfont/libXfont-1.5.1-foss-2016a.eb | 31 +++++++++ .../l/libdrm/libdrm-2.4.67-foss-2016a.eb | 28 ++++++++ .../libfontenc/libfontenc-1.1.3-foss-2016a.eb | 23 +++++++ .../libpciaccess-0.13.4-foss-2016a.eb | 26 +++++++ .../m/Mesa/Mesa-11.1.2-foss-2016a.eb | 68 +++++++++++++++++++ .../makedepend/makedepend-1.0.5-foss-2016a.eb | 20 ++++++ .../pkg-config/pkg-config-0.29-foss-2016a.eb | 27 ++++++++ .../xorg-macros-1.19.0-foss-2016a.eb | 22 ++++++ 14 files changed, 385 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb new file mode 100644 index 0000000000..3265e4fdb4 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.1.5' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-3.1.2_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb new file mode 100644 index 0000000000..4fe8f2b4dc --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb new file mode 100644 index 0000000000..0d7fd4a4a2 --- /dev/null +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'fontsproto' +version = '2.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X11 font extension wire protocol" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb new file mode 100644 index 0000000000..d26077ac1e --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'glproto' +version = '1.4.17' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb new file mode 100644 index 0000000000..19c75463d3 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdamage' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Damage extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xdamage.h', 'lib/libXdamage.%s' % SHLIB_EXT, 'lib/libXdamage.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb new file mode 100644 index 0000000000..aa11951f76 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb new file mode 100644 index 0000000000..b62ce08a63 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', '2.6.2'), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb new file mode 100644 index 0000000000..93d87d9533 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.67' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000..b21fd6654e --- /dev/null +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfontenc' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/xlibs/' +description = """X11 font encoding library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/fonts/fontenc.h', 'lib/libfontenc.%s' % SHLIB_EXT, 'lib/libfontenc.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb new file mode 100644 index 0000000000..75924f159f --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.4' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('Autotools', '20150215'), + ('xorg-macros', '1.19.0'), +] + +preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c9dd66c1c1 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.1.2' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.67'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1'), + ('LLVM', '3.7.1'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb new file mode 100644 index 0000000000..8bd95eee91 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb new file mode 100644 index 0000000000..2796515752 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 441307a0cbfd668e39a248b8a868d3edfa9e331c Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:28:31 +0100 Subject: [PATCH 201/722] add easyconfig GLPK-4.58-foss-2016a.eb --- .../g/GLPK/GLPK-4.58-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb new file mode 100644 index 0000000000..d5751eec2a --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.58' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.1.0')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 20a9dff4b702a113c5e9375b03ff2aeb68147707 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:38:33 +0100 Subject: [PATCH 202/722] add easyconfig freeglut-3.0.0-foss-2016a.eb, add easyconfig GL2PS-1.3.9-foss-2016a.eb, add easyconfig libGLU-9.0.0-foss-2016a.eb, add easyconfig libXi-1.7.6-foss-2016a.eb, add easyconfig libXmu-1.1.2-foss-2016a.eb, add easyconfig libXpm-3.5.11-foss-2016a.eb, add easyconfig libXrandr-1.5.0-foss-2016a.eb, add easyconfig randrproto-1.5.0-foss-2016a.eb --- .../f/freeglut/freeglut-3.0.0-foss-2016a.eb | 37 +++++++++++++++++++ .../g/GL2PS/GL2PS-1.3.9-foss-2016a.eb | 34 +++++++++++++++++ .../l/libGLU/libGLU-9.0.0-foss-2016a.eb | 24 ++++++++++++ .../l/libXi/libXi-1.7.6-foss-2016a.eb | 30 +++++++++++++++ .../l/libXmu/libXmu-1.1.2-foss-2016a.eb | 25 +++++++++++++ .../l/libXpm/libXpm-3.5.11-foss-2016a.eb | 22 +++++++++++ .../l/libXrandr/libXrandr-1.5.0-foss-2016a.eb | 31 ++++++++++++++++ .../randrproto/randrproto-1.5.0-foss-2016a.eb | 19 ++++++++++ 8 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb new file mode 100644 index 0000000000..aa4fa34ea2 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', '11.1.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb new file mode 100644 index 0000000000..f83060a449 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('freeglut', '3.0.0'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb new file mode 100644 index 0000000000..087bd589cb --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '11.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb new file mode 100644 index 0000000000..bd92d68db6 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' +name = 'libXi' +version = '1.7.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('inputproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c219eeb168 --- /dev/null +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXmu' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. + libXmuu is a lighter-weight version that does not depend on libXt or libXext""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libXt', '1.1.5'), + ('libXpm', '3.5.11'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%%(name)s.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb new file mode 100644 index 0000000000..1cc567cb36 --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libXpm' +version = '3.5.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [('gettext', '0.19.6')] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..b6614e79e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXrandr' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Resize, Rotate and Reflection extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('randrproto', '1.5.0'), + ('renderproto', '0.11'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrandr.%s' % SHLIB_EXT, 'lib/libXrandr.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..eab697bf89 --- /dev/null +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'randrproto' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrandr protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 40ee838e51bc76352a13168ef86058d8d4dfa8dc Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:53:41 +0100 Subject: [PATCH 203/722] add easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig gnuplot-5.0.3-foss-2016a.eb, add easyconfig GObject-Introspection-1.47.1-foss-2016a.eb, add easyconfig HarfBuzz-1.1.3-foss-2016a.eb, add easyconfig libcerf-1.4-foss-2016a.eb, add easyconfig libgd-2.1.1-foss-2016a.eb, add easyconfig Pango-1.39.0-foss-2016a.eb, add easyconfig pixman-0.34.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 49 +++++++++++++++++++ ...GObject-Introspection-1.47.1-foss-2016a.eb | 47 ++++++++++++++++++ .../g/gnuplot/gnuplot-5.0.3-foss-2016a.eb | 42 ++++++++++++++++ .../h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb | 34 +++++++++++++ .../l/libcerf/libcerf-1.4-foss-2016a.eb | 28 +++++++++++ .../l/libgd/libgd-2.1.1-foss-2016a.eb | 26 ++++++++++ .../p/Pango/Pango-1.39.0-foss-2016a.eb | 31 ++++++++++++ .../p/pixman/pixman-0.34.0-foss-2016a.eb | 20 ++++++++ 8 files changed, 277 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb new file mode 100644 index 0000000000..3684c31e54 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +glibver = '2.47.5' + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), +] +builddependencies = [ + ('renderproto', '0.11'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb new file mode 100644 index 0000000000..3c83530c29 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.47.1' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +pyver = '2.7.11' + +dependencies = [ + ('Python', pyver), + ('GLib', '2.47.5'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6'), + ('libffi', '3.2.1'), +] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb new file mode 100644 index 0000000000..7e42e00e67 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.3' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.14.6'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('libgd', '2.1.1'), + ('Pango', '1.39.0'), + ('libcerf', '1.4'), + ('Qt', '4.8.7'), +] + +configopts = '--with-qt=qt4 ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000..91db4cfacd --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6'), + ('freetype', '2.6.2'), + ('GObject-Introspection', '1.47.1') +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb new file mode 100644 index 0000000000..4f3471b4f6 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libcerf' +version = '1.4' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """libcerf is a self-contained numeric library that provides an efficient and accurate + implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TGZ] +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000..b645a00595 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.1.1' + +homepage = 'http://libgd.bitbucket.org/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/libgd/gd-libgd/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fontconfig', '2.11.94'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb new file mode 100644 index 0000000000..80529d5bda --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.39.0' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6'), + ('HarfBuzz', '1.1.3'), + ('GObject-Introspection', '1.47.1'), + ('fontconfig', '2.11.94') +] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb new file mode 100644 index 0000000000..896aab1550 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 1aa7665c7c05b88a165667d0c2b727827d2b2f70 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Tue, 22 Mar 2016 09:42:54 +0100 Subject: [PATCH 204/722] Fix string substitution issues in TAMkin easyconfig --- .../t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb index b5bff455c0..baf9ff6145 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb @@ -26,7 +26,7 @@ runtest += 'export OMP_NUM_THREADS=1; nosetests -v test' sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion], + 'dirs': ['lib/python-%(pyshortver)s/site-packages/%(namelower)s'], } moduleclass = 'chem' -- GitLab From 3cf1a6a9ba4ea24407a165db18bb20e91aa8e5da Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Tue, 22 Mar 2016 09:50:39 +0100 Subject: [PATCH 205/722] Fix typo in TAMkin easyconfig --- .../t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb index baf9ff6145..c4a906b243 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.8-intel-2015b-Python-2.7.10.eb @@ -26,7 +26,7 @@ runtest += 'export OMP_NUM_THREADS=1; nosetests -v test' sanity_check_paths = { 'files': [], - 'dirs': ['lib/python-%(pyshortver)s/site-packages/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } moduleclass = 'chem' -- GitLab From 09f2c97bc278a4a2ea87de7137f1a2234a539801 Mon Sep 17 00:00:00 2001 From: hajgato Date: Tue, 22 Mar 2016 10:26:15 +0100 Subject: [PATCH 206/722] add easyconfig FLTK-1.3.3-foss-2016a.eb, add easyconfig libXcursor-1.1.14-foss-2016a.eb, add easyconfig libXinerama-1.1.3-foss-2016a.eb, add easyconfig xineramaproto-1.2.1-foss-2016a.eb, add easyconfig xprop-1.2.2-foss-2016a.eb --- .../f/FLTK/FLTK-1.3.3-foss-2016a.eb | 37 +++++++++++++++++++ .../libXcursor-1.1.14-foss-2016a.eb | 29 +++++++++++++++ .../libXinerama-1.1.3-foss-2016a.eb | 31 ++++++++++++++++ .../xineramaproto-1.2.1-foss-2016a.eb | 19 ++++++++++ .../x/xprop/xprop-1.2.2-foss-2016a.eb | 26 +++++++++++++ 5 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000..650bf33743 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb @@ -0,0 +1,37 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.3' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + + +dependencies = [ + ('libX11', '1.6.3'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('xprop', '1.2.2'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid'], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb new file mode 100644 index 0000000000..1fc949ad4e --- /dev/null +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXcursor' +version = '1.1.14' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Cursor management library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXfixes', '5.0.1'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['include/X11/Xcursor/Xcursor.h', 'lib/libXcursor.%s' % SHLIB_EXT, 'lib/libXcursor.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000..e0a2e3d206 --- /dev/null +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXinerama' +version = '1.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Xinerama multiple monitor library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('xineramaproto', '1.2.1'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXinerama.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb new file mode 100644 index 0000000000..a40280e419 --- /dev/null +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xineramaproto' +version = '1.2.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers for xinerama" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/panoramiXproto.h'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb new file mode 100644 index 0000000000..bd60b7c873 --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.2' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftp.x.org/archive/individual/app/'] + +builddependencies = [ + ('xorg-macros', '1.19.0'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 6ccd02bdb1d7397de31d2b3f8060e559b373798e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Tue, 22 Mar 2016 11:29:53 +0100 Subject: [PATCH 207/722] Update GraphicsMagick-1.3.23-foss-2016a.eb -fpic needed by Octacve --- .../g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb index e3433e3f0b..6fa3747197 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb @@ -7,6 +7,7 @@ homepage = 'http://www.graphicsmagick.org/' description = """GraphicsMagick is the swiss army knife of image processing.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} source_urls = [ SOURCEFORGE_SOURCE, -- GitLab From 803e8384f663f340a66fa4ea79d36fc448b63b3b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 22 Mar 2016 11:32:09 +0100 Subject: [PATCH 208/722] Octave needs pic --- .../g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb index 755ecbe16c..ea37c3e81c 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb @@ -7,6 +7,7 @@ homepage = 'http://www.graphicsmagick.org/' description = """GraphicsMagick is the swiss army knife of image processing.""" toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} source_urls = [ SOURCEFORGE_SOURCE, -- GitLab From e8b93739a75d8c20e97ab89028bb9b58fb7cf0cf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 22 Mar 2016 11:53:27 +0100 Subject: [PATCH 209/722] BayeScEnv-1.1-goolf-1.4.10.eb --- .../b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..7a976185d2 --- /dev/null +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BayeScEnv' +version = '1.1' + +homepage = 'https://github.com/devillemereuil/bayescenv' +description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/devillemereuil/bayescenv/archive/'] +sources = ['v%(version)s.tar.gz'] + +start_dir = 'source' + +files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/bayescenv'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 1527993f12857255edb7ffbd9efcf6da5fd95aee Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 22 Mar 2016 21:47:20 +0000 Subject: [PATCH 210/722] Update rtracklayer to 1.30.3 --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 2 +- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index d1392d23cc..78a36e128c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -80,7 +80,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.2', bioconductor_options), + ('rtracklayer', '1.30.3', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index 60d39797ec..42093e636a 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -79,7 +79,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.2', bioconductor_options), + ('rtracklayer', '1.30.3', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), -- GitLab From d2f49d06ce3607de57e4bb93705bde9247dfdd3e Mon Sep 17 00:00:00 2001 From: fenoyc Date: Thu, 24 Mar 2016 14:25:31 +0100 Subject: [PATCH 211/722] add easyconfig OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb --- .../OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..456a180ae7 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.2' + +homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': benchmark_dirs, +} + +moduleclass = 'perf' -- GitLab From 95827494b4f314243b046063bd45bbc3eafc50f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Mar 2016 16:32:58 +0200 Subject: [PATCH 212/722] modify easyconfig GCCcore-4.9.3.eb --- easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index 268b052687..78428e12c5 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -25,7 +25,10 @@ sources = [ 'mpc-1.0.2.tar.gz', ] -builddependencies = [('binutils', '2.25')] +builddependencies = [ + ('Autotools', '20150215'), + ('binutils', '2.25'), +] patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] -- GitLab From af28806336f567e64466ba8f29d19006bfd9612a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Mar 2016 17:58:21 +0200 Subject: [PATCH 213/722] add easyconfig Saxon-HE-9.7.0.4-Java-1.7.0_79.eb --- .../Saxon-HE-9.7.0.4-Java-1.7.0_79.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb new file mode 100644 index 0000000000..eed56a9078 --- /dev/null +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'Saxon-HE' +version = '9.7.0.4' + +homepage = 'http://saxon.sourceforge.net' +description = """Open Source SAXON XSLT processor developed by Saxonica Limited.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['SaxonHE%sJ.zip' % version.replace(".","-")] + +source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s' , 'download'] + +versionsuffix = '-Java-%(javaver)s' + +dependencies = [('Java', '1.7.0_79')] + +jarfiles = ['saxon%(version_major)she.jar', 'saxon%(version_major)s-test.jar', 'saxon%(version_major)s-xqj.jar'] + +sanity_check_paths = { + 'files': jarfiles, + 'dirs': [], +} + +modextrapaths = {'CLASSPATH': jarfiles} + +moduleclass = 'devel' -- GitLab From cca33c128a3ac475714f4c99fea45fb369affbb2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Mar 2016 18:18:48 +0200 Subject: [PATCH 214/722] modify easyconfig M4-1.4.17-GCCcore-4.9.3.eb --- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb index c1c8a52948..02f06d5cfe 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 73a8f1353ac0011e1c698eee8587510a306c8898 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 24 Mar 2016 17:24:33 +0100 Subject: [PATCH 215/722] Bump FSL to intel/2016a --- .../f/FSL/FSL-5.0.9-intel-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb new file mode 100644 index 0000000000..145ff09b91 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb @@ -0,0 +1,23 @@ +name = 'FSL' +version = '5.0.9' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] + +patches = [ + 'FSL-%(version)s_makefile_fixes.patch', + 'FSL_icc_nan-inf_fix.patch', +] + +dependencies = [ + ('freeglut', '3.0.0'), + ('expat', '2.1.0'), + ('libX11', '1.6.3'), +] + +moduleclass = 'bio' -- GitLab From 4f63d5fd457e914b17b505a79ab9b948dac38ef5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 08:42:15 +0200 Subject: [PATCH 216/722] modify easyconfig Tk-8.6.4-foss-2016a-no-X11.eb --- easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb index 6f98f7076c..449ce63a29 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8') ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' -- GitLab From 7d31e07e4d50572096fe299846f23480ab5f8264 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 08:50:57 +0200 Subject: [PATCH 217/722] modify easyconfig M4-1.4.17-foss-2016a.eb --- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb index 0d030e3264..ce563e7def 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 123ca05e26b955947108f4f3a2bb414138e46df9 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 10:40:25 +0200 Subject: [PATCH 218/722] add easyconfig ant-1.9.6-Java-1.7.0_79.eb --- .../a/ant/ant-1.9.6-Java-1.7.0_79.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb new file mode 100644 index 0000000000..3ee7c5b406 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb @@ -0,0 +1,23 @@ +name = 'ant' +version = '1.9.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.7.0_79')] + +builddependencies = [('JUnit', '4.11', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9bcdda139d149aac176a17a5aa9f38b137e55d83 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 25 Mar 2016 13:48:00 +0000 Subject: [PATCH 219/722] Update Bowtie2 to 2.2.8 for recent foss --- .../b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb | 40 +++++++++++++++++++ .../b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb | 40 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb new file mode 100644 index 0000000000..29bf068b6a --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.8' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb new file mode 100644 index 0000000000..e48888855e --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.8' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' -- GitLab From 9f4fb4098262af3f3388b25be24f4eeb890274b2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:17:01 +0200 Subject: [PATCH 220/722] add easyconfig Blitz++-0.10-foss-2016a.eb --- .../b/Blitz++/Blitz++-0.10-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb new file mode 100644 index 0000000000..03886c8db9 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Blitz++' +version = '0.10' + +homepage = 'http://blitz.sourceforge.net/' +description = """Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ + with a speed comparable to Fortran implementations, while preserving an object-oriented interface""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['blitz-%(version)s.tar.gz'] +source_urls = ['https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', + 'download'] + +sanity_check_paths = { + 'files': ['lib/libblitz.a'], + 'dirs': ['include/blitz/array', + 'include/blitz/gnu', + 'include/blitz/meta', + 'include/random', + 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 020f92e1035043d6dbfcc9e9e7bfe2a80e9f9aa0 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:19:45 +0200 Subject: [PATCH 221/722] add easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig freetype-2.6.2-foss-2016a.eb, add easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig pixman-0.34.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 29 +++++++++++++++++++ .../fontconfig-2.11.94-foss-2016a.eb | 22 ++++++++++++++ .../f/freetype/freetype-2.6.2-foss-2016a.eb | 21 ++++++++++++++ .../p/pixman/pixman-0.34.0-foss-2016a.eb | 20 +++++++++++++ 4 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb new file mode 100644 index 0000000000..4afe79dcce --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb new file mode 100644 index 0000000000..d955835431 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.94' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.6.2'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb new file mode 100644 index 0000000000..3111a314be --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb new file mode 100644 index 0000000000..896aab1550 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 1d95e0d44afa8bd2a6d3dd12f779f03f377eab75 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:22:11 +0200 Subject: [PATCH 222/722] add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb --- .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' -- GitLab From a429536dc79733a15a2ecdbf335fcbed1f2990df Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:24:03 +0200 Subject: [PATCH 223/722] add easyconfig MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- ...-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb new file mode 100644 index 0000000000..a11de24d4f --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus' +version = '7.0.67' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['stable_release-%s.zip' % version.replace('.','-')] + +dependencies = [ + ('Java', '1.7.0_79', '', True), + ('Python', '2.7.11'), + ('HDF5', '1.8.16'), + ('libxml2', '2.9.3', '-Python-%(pyver)s') +] + +configopts = '--with-jdk=$JAVA_HOME' + +preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' + +buildopts = '-j 1' + +moduleclass = 'data' -- GitLab From 0f7f918444396849cefb3ddd10ec622ceb292c8a Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 28 Mar 2016 13:42:38 -0500 Subject: [PATCH 224/722] Adding Email to the easyconfig --- easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb index aa280fb576..6d1dad133e 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb @@ -1,5 +1,6 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Ravi Tripathi +# Email: ravi89@uab.edu easyblock = "Binary" -- GitLab From 7665efa01e6c846d6fcc6299b62552125d23d5de Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 28 Mar 2016 13:45:45 -0500 Subject: [PATCH 225/722] Adding email to shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb Easyconfig file --- .../s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb index a71ba8d96d..7441bd58af 100644 --- a/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb +++ b/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb @@ -1,5 +1,6 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Ravi Tripathi +# Email: ravi89@uab.edu easyblock = "Binary" -- GitLab From 4bc1fe85404268c258d800beb130fe6597928b40 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 28 Mar 2016 14:07:21 -0500 Subject: [PATCH 226/722] Adding an Easyconfig file for MRICron built on 06/22/2015 --- .../m/mricron/mricron-062215-linux_x86_64.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb diff --git a/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb b/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb new file mode 100644 index 0000000000..a7fb738545 --- /dev/null +++ b/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Binary" + +name = 'mricron' +version = '062215' +versionsuffix = '_linux_x86_64' + +homepage = 'http://www.mccauslandcenter.sc.edu/mricro/mricron/' +description = """ MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] +sources = ['lx.zip'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "unzip lx.zip && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], + 'dirs': ["example", "lut", "templates"] +} + +moduleclass = 'bio' -- GitLab From cff82a7a7cce953ae7c746a6227a1e01777bf81f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 28 Mar 2016 23:40:39 +0100 Subject: [PATCH 227/722] Use latest numpy and fix tests --- .../r/RSeQC/RSeQC-2.6.3-foss-2015b.eb | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb index c0f1f917f6..c33eb72992 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb @@ -1,3 +1,7 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + easyblock = 'PythonPackage' name = 'RSeQC' @@ -16,20 +20,22 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCE_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] -patches = [] - -Python = 'Python' +python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('R', '3.2.3'), - ('numpy', '1.9.2'), + ('numpy', '1.10.1', versionsuffix), ] +runtest = "python setup.py test" + sanity_check_paths = { 'files': [], - 'dirs': ["."] + 'dirs': ["bin", "lib"] } +options = {'modulename': 'qcmodule'} + moduleclass = 'bio' -- GitLab From 9403a1c1ed2e243ded00fd181b7c3e74f6f8061c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 28 Mar 2016 23:48:28 +0100 Subject: [PATCH 228/722] Remove obsolete numpy dep for RSeQC --- .../numpy-1.9.2-foss-2015b-Python-2.7.10.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb deleted file mode 100644 index f55df325cf..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'numpy' -version = '1.9.2' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'foss', 'version': '2015b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['numpy-1.8.0-mkl.patch'] - -python = 'Python' -pyver = '2.7.10' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('SuiteSparse', '4.4.5', '-METIS-5.1.0'), -] - -moduleclass = 'math' -- GitLab From bda5cb872c43f93c6f7207cdf42e96364661b7a0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Mar 2016 07:45:09 +0100 Subject: [PATCH 229/722] Add BEDTools 2.25.0 to foss-2015b and foss-2016a --- .../b/BEDTools/BEDTools-2.25.0-foss-2015b.eb | 33 +++++++++++++++++++ .../b/BEDTools/BEDTools-2.25.0-foss-2016a.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb new file mode 100644 index 0000000000..50f76cdae7 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.25.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb new file mode 100644 index 0000000000..89147e0b20 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.25.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 9e31cc2f81179ae76942ac50899220609c8d5438 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Mar 2016 07:59:12 +0100 Subject: [PATCH 230/722] Fix version, description, sanity check and build options --- .../s/Subread/Subread-1.5.0p1-foss-2015b.eb | 28 +++++++++---------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb index 245a7b2f5a..4fd69f051e 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb @@ -1,30 +1,28 @@ -# Note: -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# It was auto-generated based on a template easyconfig, so it should be used with care. +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute easyblock = 'MakeCp' name = 'Subread' -version = '1.5.0p1' +version = '1.5.0-p1' homepage = 'http://subread.sourceforge.net/' -description = """TEMPLATE DESCRIPTION""" +description = """High performance read alignment, quantification and mutation discovery""" -# toolchain name should be 'TEMPLATE' if this is a template, so EasyBuild knows and is willing to use it as a template toolchain = {'name': 'foss', 'version': '2015b'} -toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... -# For sources line to work correctly with --try-software-version, you MUST employ %s OR use a construct like SOURCE_TAR_GZ -sources = ['%(namelower)s-%version)s-source.tar.gz'] -source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -patches = [] +prebuildopts = 'cd src;' +buildopts = '-f Makefile.Linux' + +files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] -dependencies = [] -# The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['LICENSE', 'README.txt'], + 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] } moduleclass = 'bio' -- GitLab From 4b1b8e1b10c5d5378efc01381b9deb998f20c8f5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Mar 2016 08:02:18 +0100 Subject: [PATCH 231/722] Add foss-2016a port of Subread --- .../s/Subread/Subread-1.5.0p1-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb new file mode 100644 index 0000000000..1312eb0648 --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'MakeCp' + +name = 'Subread' +version = '1.5.0-p1' + +homepage = 'http://subread.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] + +prebuildopts = 'cd src;' +buildopts = '-f Makefile.Linux' + +files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] + + +sanity_check_paths = { + 'files': ['LICENSE', 'README.txt'], + 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] +} + +moduleclass = 'bio' -- GitLab From 8466e1b77b8a8c23b3a659045371f9db70b304f4 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Tue, 29 Mar 2016 22:02:06 +0200 Subject: [PATCH 232/722] New `.eb` files for LinBox 1.4.0, FFLAS-FFPACK 2.2.0, and Givaro 4.0.1 --- .../FFLAS-FFPACK-2.2.0-foss-2016a.eb | 70 +++++++++++++++++++ .../g/Givaro/Givaro-4.0.1-foss-2016a.eb | 45 ++++++++++++ .../l/LinBox/LinBox-1.4.0-foss-2016a.eb | 70 +++++++++++++++++++ 3 files changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb new file mode 100644 index 0000000000..382acef001 --- /dev/null +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -0,0 +1,70 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'FFLAS-FFPACK' +version = '2.2.0' + +homepage = 'https://linbox-team.github.io/fflas-ffpack/' +description = "Finite Field Linear Algebra Subroutines / Package" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v2.2.0.zip'] +source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] + +builddependencies = [ + ('Autoconf', '2.69', '', True), + ('Automake', '1.15', '', True), + ('libtool', '2.4.6', '', True), +] +dependencies = [ + ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), + ('Givaro', '4.0.1'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' + +parallel = 4 + +unwanted_env_vars = {} +start_dir = '%(builddir)s/%(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.8.0dev0", + "easybuild-easyblocks_version": "2.8.0dev0", + "timestamp": 1459270041, + "build_time": 30.84, + "install_size": 1762928, + "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'FFLAS-FFPACK-2.2.0-foss-2015a.eb'], + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), + "core_count": 4, + "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", + "cpu_speed": 2400.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", + "glibc_version": "2.21", + "hostname": "xenia", + "os_name": "ubuntu", + "os_type": "Linux", + "os_version": "15.10", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", + "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", + "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", +}] diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb new file mode 100644 index 0000000000..56ed27ad72 --- /dev/null +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'Givaro' +version = '4.0.1' + +homepage = 'http://givaro.forge.imag.fr/' +description = "C++ library for arithmetic and algebraic computations" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v4.0.1.zip'] +source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] + +builddependencies = [ + ('Autoconf', '2.69', '', True), + ('Automake', '1.15', '', True), + ('libtool', '2.4.6', '', True), +] +dependencies = [ + ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = "--with-gmp=$EBROOTGMP --enable-inline" + +parallel = 4 + +unwanted_env_vars = {} +start_dir = '%(builddir)s/%(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s-config.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb new file mode 100644 index 0000000000..042673b61a --- /dev/null +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -0,0 +1,70 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'LinBox' +version = '1.4.0' + +homepage = 'http://linalg.org/' +description = "C++ library for exact, high-performance linear algebra" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v1.4.0.zip'] +source_urls = ['https://github.com/%(namelower)s-team/%(namelower)s/archive'] + +builddependencies = [ + ('Autoconf', '2.69', '', True), + ('Automake', '1.15', '', True), + ('libtool', '2.4.6', '', True), +] +dependencies = [ + ('FFLAS-FFPACK', '2.2.0'), + ('Givaro', '4.0.1'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = "--with-givaro=$EBROOTGIVARO --with-fflas-ffpack=$EBROOTFFLASMINFFPACK --enable-openmp" + +parallel = 4 + +unwanted_env_vars = {} +start_dir = '%(builddir)s/%(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s-config.h', 'lib/liblinbox.a'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.8.0dev0", + "easybuild-easyblocks_version": "2.8.0dev0", + "timestamp": 1459270157, + "build_time": 64.4, + "install_size": 8769443, + "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'LinBox-1.4.0-foss-2015a.eb'], + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), + "core_count": 4, + "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", + "cpu_speed": 2400.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", + "glibc_version": "2.21", + "hostname": "xenia", + "os_name": "ubuntu", + "os_type": "Linux", + "os_version": "15.10", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", + "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", + "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", +}] -- GitLab From 842135094fa8af11889df5460b3aa58906661c11 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Tue, 29 Mar 2016 22:33:16 +0200 Subject: [PATCH 233/722] Remove "buildstatistics" section that sneaked in --- .../FFLAS-FFPACK-2.2.0-foss-2016a.eb | 24 ------------------- .../l/LinBox/LinBox-1.4.0-foss-2016a.eb | 24 ------------------- 2 files changed, 48 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 382acef001..153536ed7b 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -44,27 +44,3 @@ sanity_check_paths = { } moduleclass = 'math' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.8.0dev0", - "easybuild-easyblocks_version": "2.8.0dev0", - "timestamp": 1459270041, - "build_time": 30.84, - "install_size": 1762928, - "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'FFLAS-FFPACK-2.2.0-foss-2015a.eb'], - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), - "core_count": 4, - "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", - "cpu_speed": 2400.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", - "glibc_version": "2.21", - "hostname": "xenia", - "os_name": "ubuntu", - "os_type": "Linux", - "os_version": "15.10", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", - "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", - "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", -}] diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index 042673b61a..df00b437d1 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -44,27 +44,3 @@ sanity_check_paths = { } moduleclass = 'math' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.8.0dev0", - "easybuild-easyblocks_version": "2.8.0dev0", - "timestamp": 1459270157, - "build_time": 64.4, - "install_size": 8769443, - "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'LinBox-1.4.0-foss-2015a.eb'], - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), - "core_count": 4, - "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", - "cpu_speed": 2400.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", - "glibc_version": "2.21", - "hostname": "xenia", - "os_name": "ubuntu", - "os_type": "Linux", - "os_version": "15.10", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", - "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", - "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", -}] -- GitLab From 1f0c0f48cdee7708fbcbbd1584e5539528823e2f Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Tue, 29 Mar 2016 15:42:59 -0700 Subject: [PATCH 234/722] add Nvidia OptiX 3.8.0 easyconfig --- .../o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..db096d2117 --- /dev/null +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors:: Stephane Thiell +## +easyblock = 'Binary' +name = 'OptiX' +version = '3.8.0' + +homepage = 'https://developer.nvidia.com/optix' +description = """OptiX is NVIDIA SDK for easy ray tracing performance. + It provides a simple framework for accessing the GPU’s massive ray tracing + power using state-of-the-art GPU algorithms.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +#source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.run'] + +checksums = [ + 'ecf63cf32b87defa36d3cd283d085314', # NVIDIA-OptiX-SDK-3.8.0-linux64.run +] + +install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.so", "lib64/liboptixu.so"], + 'dirs': [] +} + +modextravars = { 'OPTIX_HOME': '%(installdir)s' } + +moduleclass = 'vis' -- GitLab From a192c8e8addf0c4d566a728cca056b438cc1e3fb Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 10:41:23 +0200 Subject: [PATCH 235/722] Edits suggested by @boegel and general cleanup. Some cruft was added by EB as a result of saving back the file, and it gets dutifully removed now. (Well, hopefully!) --- .../FFLAS-FFPACK-2.2.0-foss-2016a.eb | 24 ++++++++----------- .../g/Givaro/Givaro-4.0.1-foss-2016a.eb | 21 +++++++--------- .../l/LinBox/LinBox-1.4.0-foss-2016a.eb | 21 +++++++--------- 3 files changed, 26 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 153536ed7b..282843bbc7 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -17,30 +17,26 @@ description = "Finite Field Linear Algebra Subroutines / Package" toolchain = {'version': '2016a', 'name': 'foss'} -sources = ['v2.2.0.zip'] -source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/fflas-ffpack/archive'] builddependencies = [ - ('Autoconf', '2.69', '', True), - ('Automake', '1.15', '', True), - ('libtool', '2.4.6', '', True), + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('libtool', '2.4.6'), ] dependencies = [ - ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), + ('GMP', '6.1.0'), ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " -configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' - -parallel = 4 - -unwanted_env_vars = {} -start_dir = '%(builddir)s/%(namelower)s-%(version)s/' +configopts = ('--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' + ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp') sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s.h'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/fflas-ffpack-config', 'include/fflas-ffpack/fflas-ffpack.h'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb index 56ed27ad72..fe391b51b5 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -17,29 +17,24 @@ description = "C++ library for arithmetic and algebraic computations" toolchain = {'version': '2016a', 'name': 'foss'} -sources = ['v4.0.1.zip'] -source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/givaro/archive'] builddependencies = [ - ('Autoconf', '2.69', '', True), - ('Automake', '1.15', '', True), - ('libtool', '2.4.6', '', True), + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('libtool', '2.4.6'), ] dependencies = [ - ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), + ('GMP', '6.1.0'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " configopts = "--with-gmp=$EBROOTGMP --enable-inline" -parallel = 4 - -unwanted_env_vars = {} -start_dir = '%(builddir)s/%(namelower)s-%(version)s/' - sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s-config.h'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/givaro-config', 'include/givaro-config.h'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index df00b437d1..4d00ba2bf0 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -17,30 +17,25 @@ description = "C++ library for exact, high-performance linear algebra" toolchain = {'version': '2016a', 'name': 'foss'} -sources = ['v1.4.0.zip'] -source_urls = ['https://github.com/%(namelower)s-team/%(namelower)s/archive'] +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/linbox/archive'] builddependencies = [ - ('Autoconf', '2.69', '', True), - ('Automake', '1.15', '', True), - ('libtool', '2.4.6', '', True), + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('libtool', '2.4.6'), ] dependencies = [ ('FFLAS-FFPACK', '2.2.0'), - ('Givaro', '4.0.1'), + ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " configopts = "--with-givaro=$EBROOTGIVARO --with-fflas-ffpack=$EBROOTFFLASMINFFPACK --enable-openmp" -parallel = 4 - -unwanted_env_vars = {} -start_dir = '%(builddir)s/%(namelower)s-%(version)s/' - sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s-config.h', 'lib/liblinbox.a'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/linbox-config', 'include/linbox/linbox-config.h', 'lib/liblinbox.a'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' -- GitLab From e0e12f2bcce4f121fbc00a1d3787a62d35c8766e Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 11:00:47 +0200 Subject: [PATCH 236/722] Use `Autotools` bundle instead of depending on each tool separately. --- .../f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb | 4 +--- easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb | 4 +--- easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb | 4 +--- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 282843bbc7..94cd13bd81 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -21,9 +21,7 @@ sources = ['v%(version)s.zip'] source_urls = ['https://github.com/linbox-team/fflas-ffpack/archive'] builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15'), - ('libtool', '2.4.6'), + ('Autotools', '20150215'), ] dependencies = [ ('GMP', '6.1.0'), diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb index fe391b51b5..4f0fbad866 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -21,9 +21,7 @@ sources = ['v%(version)s.zip'] source_urls = ['https://github.com/linbox-team/givaro/archive'] builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15'), - ('libtool', '2.4.6'), + ('Autotools', '20150215'), ] dependencies = [ ('GMP', '6.1.0'), diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index 4d00ba2bf0..640a495db8 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -21,9 +21,7 @@ sources = ['v%(version)s.zip'] source_urls = ['https://github.com/linbox-team/linbox/archive'] builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15'), - ('libtool', '2.4.6'), + ('Autotools', '20150215'), ] dependencies = [ ('FFLAS-FFPACK', '2.2.0'), -- GitLab From 236a8879552482ac855d3c1fbbf69c0089fb53d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 12:47:31 +0200 Subject: [PATCH 237/722] {lang}[intel/2016a] numba 0.24.0 w/ Python 2.7.11 & 3.5.1 --- .../llvmlite-0.9.0_fix-ffi-Makefile.patch | 29 +++++++++++++ .../numba-0.24.0-intel-2016a-Python-2.7.11.eb | 41 +++++++++++++++++++ .../numba-0.24.0-intel-2016a-Python-3.5.1.eb | 41 +++++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch create mode 100644 easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch new file mode 100644 index 0000000000..7a74cc0623 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch @@ -0,0 +1,29 @@ +don't use -static-libstdc++, causing problems like "glibc detected *** python: free(): invalid pointer" +cfr. https://github.com/numba/llvmlite/issues/93; +don't hardcode -lLLVMOProfileJIT, not required anymore +cfr. https://github.com/numba/llvmlite/issues/121 +author: Kenneth Hoste (HPC-UGent) +--- llvmlite-0.9.0/ffi/Makefile.linux.orig 2016-01-26 15:11:43.000000000 +0100 ++++ llvmlite-0.9.0/ffi/Makefile.linux 2016-03-30 12:41:34.102307156 +0200 +@@ -4,9 +4,7 @@ + # -flto and --exclude-libs allow us to remove those parts of LLVM we don't use + CXXFLAGS = $(LLVM_CXXFLAGS) -flto + LDFLAGS = $(LLVM_LDFLAGS) -flto -Wl,--exclude-libs=ALL +-# Need to add LLVMOProfileJIT by hand +-# see https://llvm.org/bugs/show_bug.cgi?id=25091 +-LIBS = $(LLVM_LIBS) -lLLVMOProfileJIT ++LIBS = $(LLVM_LIBS) + SRC = assembly.cpp bitcode.cpp core.cpp initfini.cpp module.cpp value.cpp \ + executionengine.cpp transforms.cpp passmanagers.cpp targets.cpp dylib.cpp \ + linker.cpp +@@ -15,9 +13,7 @@ + all: $(OUTPUT) + + $(OUTPUT): $(SRC) +- # static-libstdc++ avoids runtime dependencies on a +- # particular libstdc++ version. +- $(CXX) -static-libstdc++ -shared $(CXXFLAGS) $(SRC) -o $(OUTPUT) $(LDFLAGS) $(LIBS) ++ $(CXX) -shared $(CXXFLAGS) $(SRC) -o $(OUTPUT) $(LDFLAGS) $(LIBS) + + clean: + rm -rf test diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0ddf57da7d --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,41 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.24.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('LLVM', '3.7.1'), +] + +exts_list = [ + ('llvmlite', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..e0e36eeb79 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,41 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.24.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.1'), + ('LLVM', '3.7.1'), +] + +exts_list = [ + ('llvmlite', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' -- GitLab From a45e7509603391b8a42eb3f1d333cfd902bfefc9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 12:53:43 +0200 Subject: [PATCH 238/722] use right patch file for llvmlite --- .../n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb | 2 +- .../n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb index 0ddf57da7d..1ed8278597 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ dependencies = [ exts_list = [ ('llvmlite', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], - 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + 'patches': ['llvmlite-0.9.0_fix-ffi-Makefile.patch'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb index e0e36eeb79..c11e1bdb17 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb @@ -21,7 +21,7 @@ dependencies = [ exts_list = [ ('llvmlite', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], - 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + 'patches': ['llvmlite-0.9.0_fix-ffi-Makefile.patch'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], -- GitLab From ed68b28d57a933a0570d61aa9a8a7c8d40ebffb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 15:09:50 +0200 Subject: [PATCH 239/722] {system}[intel/2016a] file 5.25 + enhance sanity check --- .../easyconfigs/f/file/file-5.17-GCC-4.8.2.eb | 8 +++--- .../f/file/file-5.25-intel-2016a.eb | 25 +++++++++++++++++++ 2 files changed, 29 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb b/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb index 63db8305d5..bca5d69508 100644 --- a/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb @@ -12,14 +12,14 @@ homepage = 'http://www.darwinsys.com/file/' description = """The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains.""" +toolchain = {'name': 'GCC', 'version': '4.8.2'} + source_urls = ['ftp://ftp.astron.com/pub/file/'] sources = [SOURCE_TAR_GZ] -toolchain = {'name': 'GCC', 'version': '4.8.2'} - sanity_check_paths = { - 'files': ['bin/file'], - 'dirs': [] + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] } moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb b/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb new file mode 100644 index 0000000000..61f8e29397 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.25' + +homepage = 'http://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' -- GitLab From b92eaf3eac50f53ac2b688a53b821a92f797371a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 16:02:50 +0200 Subject: [PATCH 240/722] add easyconfig Java-1.8.0_77.eb --- easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb new file mode 100644 index 0000000000..fa48d66cd4 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_77' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 3df8b5b4e3a15448caa4ef4b023b13d4ee1f31a8 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 16:42:55 +0200 Subject: [PATCH 241/722] More style edits suggested by @boegel --- .../f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb | 8 ++++---- easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 94cd13bd81..da99f9d5b8 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -24,17 +24,17 @@ builddependencies = [ ('Autotools', '20150215'), ] dependencies = [ - ('GMP', '6.1.0'), + ('GMP', '6.1.0'), ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " -configopts = ('--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' - ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp') +configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' +configopts += ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' sanity_check_paths = { 'files': ['bin/fflas-ffpack-config', 'include/fflas-ffpack/fflas-ffpack.h'], - 'dirs': ['bin', 'include', 'lib'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb index 4f0fbad866..22ad6d392a 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -32,7 +32,7 @@ configopts = "--with-gmp=$EBROOTGMP --enable-inline" sanity_check_paths = { 'files': ['bin/givaro-config', 'include/givaro-config.h'], - 'dirs': ['bin', 'include', 'lib'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index 640a495db8..f0951b2b35 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ ('FFLAS-FFPACK', '2.2.0'), - ('Givaro', '4.0.1'), + ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " @@ -33,7 +33,7 @@ configopts = "--with-givaro=$EBROOTGIVARO --with-fflas-ffpack=$EBROOTFFLASMINFFP sanity_check_paths = { 'files': ['bin/linbox-config', 'include/linbox/linbox-config.h', 'lib/liblinbox.a'], - 'dirs': ['bin', 'include', 'lib'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' -- GitLab From 29197e7d989d93758bf1fb0ee678de15f6d0f592 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 16:47:02 +0200 Subject: [PATCH 242/722] add easyconfig NGS-1.2.3-intel-2016a.eb --- .../n/NGS/NGS-1.2.3-intel-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb new file mode 100644 index 0000000000..ed0e37836c --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.2.3' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Java', '1.8.0_77', '', True)] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' -- GitLab From 96afcdd6c2a927d1aaf5e9364af131a34c1e0162 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 22:22:41 +0200 Subject: [PATCH 243/722] Use `env` wherever `preconfigopts is used to set environmental variables. Without `env`, we are relying on a syntactical feature of Bourne-type shells; the `env` utility guarantees that the command-line will continue to work even with other shells (e.g., `tcsh`). --- .../easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb | 2 +- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 2 +- .../c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb | 2 +- .../Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb | 2 +- .../g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb | 2 +- .../easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb | 2 +- .../l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb | 2 +- .../l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb | 2 +- .../l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb | 2 +- .../l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb | 2 +- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb | 2 +- .../r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 2 +- .../v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 2 +- 105 files changed, 105 insertions(+), 105 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb index 20c30c8e62..6b5c1c6d52 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb @@ -31,7 +31,7 @@ dependencies = [ ('Boost', '1.58.0', versionsuffix), ] -preconfigopts = 'CPPFLAGS=-I$EBROOTSPARSEHASH/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTSPARSEHASH/include' sanity_check_paths = { 'files': ["bin/ABYSS", "bin/ABYSS-P"], diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb index 13ae69456f..916fcd7e48 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb index 5144a9afc9..97e5c8330b 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb index 3b963e0d7e..74f9dffca6 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb index f6a35a3dc0..efd5845e70 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 608c44a155..35e328daad 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -21,7 +21,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 17ecd5c190..6c55f76694 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -20,7 +20,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 61254037e0..6f9a318360 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -21,7 +21,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index 0007322f1f..ef80ad6bb5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -20,7 +20,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index e6f5a84c78..b8fa0b77ca 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -21,7 +21,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 8efdae380a..9ec199023d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -22,7 +22,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index b6d188a41b..63837a712c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -21,7 +21,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib # further, add the system library path in the rpath: this should 'harden' the # resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' prebuildopts = preconfigopts # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 40e3ccc1a8..cfcfe38d3d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib # further, add the system library path in the rpath: this should 'harden' the # resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' prebuildopts = preconfigopts # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index 501824903b..7b8dca8554 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -34,7 +34,7 @@ patches = [ 'cufflinks-1.x-ldflags.patch' ] -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb index d258537699..2ef873d2da 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb @@ -30,7 +30,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb index 645f94a833..25b9208f0e 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb @@ -32,7 +32,7 @@ dependencies = [ patches = ['Cufflinks_GCC-4.7.patch'] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb index 799e9172ba..9c37cd717b 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb @@ -34,7 +34,7 @@ dependencies = [ configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' configopts += ' --enable-intel64 ' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb index 991b5a4c8b..6751cec530 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb @@ -33,7 +33,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb index d0372e6f70..6ac33d77d4 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb index 2741497a4d..e368245a6c 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb index 0a4b6fa7ab..fe15c228e1 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb @@ -18,7 +18,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb index 43da714323..50fce481a6 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb @@ -19,7 +19,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb index 38e9d1ce03..8360322002 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb @@ -21,7 +21,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I${EBROOTEIGEN}/include' +preconfigopts = 'env CPPFLAGS=-I${EBROOTEIGEN}/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb index ffd2e3a7a6..4bcdb9773b 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb index 8f6396f5b8..7a4d21e078 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb index ee472aa372..4e298ad677 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb index ef2423ee53..4b6a000d12 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb index c0f9f1c6d8..9445690c85 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb index 384aa93ebf..1f66eb79d7 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb index 048ac9570d..8bc580fd82 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb index cc9e86a7d0..8c554c3e24 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb @@ -15,7 +15,7 @@ source_urls = ['http://www.prevanders.net'] dependencies = [('libelf', '0.8.13')] with_configure = True -preconfigopts = 'CFLAGS="-fPIC $CFLAGS" ' +preconfigopts = 'env CFLAGS="-fPIC $CFLAGS" ' configopts = "--enable-shared " # This is dirty but libdwarf cannot find it's own library in the build process... diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb index 6ac9b7d5c3..01c9c7b5d7 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb index a021127537..3c63b87470 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb index 11090d4b7a..437954d342 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb index f66aff6454..f0291301fc 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb index f03e2b9b60..e43c36e89c 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb index 33c34a406a..834a292992 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb index 7e3d115240..c3e51b6854 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb index ce77f3502c..8f259d339a 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb index e28f16cff6..5f22d77a36 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb index 2a5e9c8d05..ea05edcced 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb index 4281029487..1af83efe66 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb index 2ac72299c5..c0a23d9702 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb index 17ca0fce10..084f645370 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb index 8d2ea29b4c..f0751a5aa2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb index aea7099ee4..0ae01c0783 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb index 7216c9ca1c..39cc896311 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb index 6589e3ba7c..9a9c4dd1a0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb index a36ac06d74..245f1b2b64 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb index 4425696364..8e8d97c9af 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb index 8892dfc907..0e2ab07ab0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb index 7778abffff..c6a66c33d9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb index 157a15b6bb..f765c40888 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb index 6a9bcf9cdd..f13cdef958 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb index c5324cbad1..f5f1c5bd47 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb index b07b7634b9..5c9d193cce 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb index 853816b19b..596222a189 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb index 26cadb84b9..2ed024170c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb index 055d457da0..fd8d7fabf0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb index 6f9a153abf..35b967c78d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb index a4bce470a5..54fd902c42 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb index 8003f03676..12e011a8ed 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb index 15a227218e..18ebd1a1e7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb index 9236fd84d0..cdb4bf6f5a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb index 7435fb5029..0f7e912805 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb index a669b4f5be..27560c2cd2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb index a120dd4307..7ca975dc76 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb index 883868add2..b30099a775 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb index d828f262a5..712eabaeda 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb index 252a86c527..667201ed1a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb @@ -17,7 +17,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb index afd0f9f313..55974b6b67 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb index 46e89b5a96..68d5cccacb 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb @@ -19,7 +19,7 @@ builddependencies = [('binutils', '2.25')] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb index 05d8476935..d726fb4329 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb index 362df4f9bd..2745ab8557 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 763ccd9488..c856b61000 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb index d3b76459b6..b5740c5333 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb index 66ecad79ff..4bbd90baa7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb index 037141ab77..e33a1ae239 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb index fb2145ca85..675e8c38cd 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb index 8845b7c009..dbc0087596 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb index 793dcaf0af..cbb20595ce 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb index e594babc96..7ecfe2dc0a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb index ec5413615c..3c009a2b02 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb index 35af50be83..84703a1b03 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb @@ -20,7 +20,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb index 2db2e85326..fdf5247663 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb @@ -20,7 +20,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb index c9c675d484..fb685e3854 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb index 46eef59b19..68d21572c3 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb index 583b41298f..76b828f76d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb index 3e67c20449..9539bb724f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb index 2c8752c400..051672a6f2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb index de76493eec..fa9c58b0b8 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb index 0762f90f29..5b1cb39b0a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb index 5bcb7de6da..b08de1e59f 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb @@ -15,6 +15,6 @@ checksums = ['5dc58ed08fd3142c260b70fe297e127c'] builddependencies = [('Bison', '2.7')] # the hydra launcher start's before LD_LIBRARY_PATH is forwarded, so we provide this hint on where to find some libs -preconfigopts = 'LDFLAGS="-Wl,-rpath,$EBROOTICC/compiler/lib/intel64 $LDFLAGS"' +preconfigopts = 'env LDFLAGS="-Wl,-rpath,$EBROOTICC/compiler/lib/intel64 $LDFLAGS"' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb index 9cac08c076..3b2363cdf9 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb index c6b4f4fabd..b547dd35fb 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb index f3480b9f42..2be6013ea4 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb index a8664f7399..c2a88ca7fa 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index bcf88e98c9..a7caba4fae 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] configopts = ' --enable-unicode=ucs4 ' -preconfigopts = ' LDFLAGS="-lstdc++" ' +preconfigopts = 'env LDFLAGS="-lstdc++" ' # libffi build in python is still broken, see http://bugs.python.org/issue4130 patches = ['python-2.7_libffi-include-xmmintrin.patch'] diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb index 4f0b4fda48..05baffbd16 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb @@ -34,7 +34,7 @@ dependencies = [ ] # use external ZLIB -preconfigopts = 'ZLIB=$EBROOTZLIB ' +preconfigopts = 'env ZLIB=$EBROOTZLIB ' # architecture arch = 'linuxx8664icc' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index 59556c19fd..fc6f18713c 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -32,7 +32,7 @@ dependencies = [ ] # use external ZLIB -preconfigopts = 'ZLIB=$EBROOTZLIB ' +preconfigopts = 'env ZLIB=$EBROOTZLIB ' # architecture arch = 'linuxx8664icc' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb index 740784c812..795671412f 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb @@ -29,7 +29,7 @@ source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 327bd773eb..1e20cf23ec 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -29,7 +29,7 @@ source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb index 375b58016f..b7723d7af3 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb @@ -31,7 +31,7 @@ patches = ['ViennaRNA_ictce-pragma.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index 316c43df98..a66be3332b 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -32,7 +32,7 @@ patches = ['ViennaRNA_ictce-pragma.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index d9a8ebec92..664ec56172 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -31,7 +31,7 @@ patches = ['ViennaRNA-2.1.6_ictce.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', -- GitLab From 53eadadc575930bd0d5729d2239c3df8d70316fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 10:16:47 +0200 Subject: [PATCH 244/722] add easyconfig ncbi-vdb-2.5.8-1-intel-2016a.eb --- .../ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb new file mode 100644 index 0000000000..4197805f9e --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.5.8-1' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libxml2', '2.9.3'), + ('file', '5.25'), # provides libmagic + ('HDF5', '1.8.16'), + ('NGS', '1.2.3'), +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-vdb.%s' % SHLIB_EXT, 'lib64/libncbi-vdb.%s' % SHLIB_EXT), + ('lib/libncbi-wvdb.%s' % SHLIB_EXT, 'lib64/libncbi-wvdb.%s' % SHLIB_EXT), + ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a'), ('lib/libncbi-vdb.a', 'lib64/libncbi-vdb.a'), + ('lib/libncbi-wvdb.a', 'lib64/libncbi-wvdb.a')], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 0af7e722e8f3aa0b28b12b62424772425ad587bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 11:57:16 +0200 Subject: [PATCH 245/722] add easyconfig HISAT2-2.0.3-beta-intel-2016a.eb --- .../h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb new file mode 100644 index 0000000000..c08c2f92a9 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.3-beta' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +checksums = ['deb29e32e48045b2f970fb999946b411'] + +dependencies = [ + ('NGS', '1.2.3'), + ('ncbi-vdb', '2.5.8-1'), +] + +buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e0707b966ea23e736726488c4039e47960fc9bbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 12:22:31 +0200 Subject: [PATCH 246/722] modify easyconfig HISAT2-2.0.3-beta-intel-2016a.eb --- easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb index c08c2f92a9..ab9ee05adb 100644 --- a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncbi-vdb', '2.5.8-1'), ] -buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB" +buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] -- GitLab From 3120311ff75bf2561aa7b6cfee5f6f3456966d47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 12:47:43 +0200 Subject: [PATCH 247/722] {bio}[intel/2016a] NGS-Python 1.2.3 --- ...-Python-1.2.3-intel-2016a-Python-2.7.11.eb | 46 +++++++++++++++++++ .../NGS-Python-1.2.3_fix-prefix.patch | 13 ++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..94dc61a1a7 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'NGS-Python' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = ['NGS-Python-%(version)s_fix-prefix.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('NGS', version), + ('ncbi-vdb', '2.5.8-1'), +] + +preconfigopts = "cd ngs-python && " + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS " +configopts += "--with-ncbi-vdb-prefix=$EBROOTNCBIMINVDB" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-python' +installopts = "-C ngs-python" + +parallel = 1 + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python2.7/site-packages', 'share/examples-python'], +} + +sanity_check_commands = [('python', "-c 'import ngs'")] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch new file mode 100644 index 0000000000..60411ef541 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch @@ -0,0 +1,13 @@ +correctly specify prefix to install NGS-Python package to +author: Kenneth Hoste (HPC-UGent) +--- ngs-1.2.3/ngs-python/Makefile.python.orig 2016-03-31 12:34:54.124551782 +0200 ++++ ngs-1.2.3/ngs-python/Makefile.python 2016-03-31 12:37:01.515699327 +0200 +@@ -82,7 +82,7 @@ + + else + @ echo "Installing ngs package..." +- @ python setup.py -q install --user ++ @ python setup.py -q install --prefix $(INST_PYTHONDIR) + endif + + ifneq (, $(NGS_LIBDIR)) -- GitLab From af36210e03039665d0ac97e321a93585e12c0f2a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 12:11:56 +0100 Subject: [PATCH 248/722] Add explicit Python dep and rename to reflect that --- ...6.3-foss-2015b.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/r/RSeQC/{RSeQC-2.6.3-foss-2015b.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb} (98%) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb similarity index 98% rename from easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb rename to easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb index c33eb72992..4fc2b27c34 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb @@ -26,6 +26,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('R', '3.2.3'), + (python, pyver), ('numpy', '1.10.1', versionsuffix), ] -- GitLab From 311923d8aa7e6717ee43fa4414580f5e4cf9f605 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Thu, 31 Mar 2016 13:11:59 +0200 Subject: [PATCH 249/722] Use `env` wherever `preinstallopts is used to set environmental variables. --- .../p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb index 699eafed53..ab6efabad7 100644 --- a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ skipsteps = ['configure', 'build'] # redefine $HOME to specify installation prefix O_o -preinstallopts = "HOME=%(installdir)s make local &&" +preinstallopts = "env HOME=%(installdir)s make local &&" sanity_check_paths = { 'files': ['p4vasp/bin/p4v', 'p4vasp/lib/libODP.a', 'p4vasp/lib/libp4vasp.a'], -- GitLab From 2fb5725bfc6410ec511fdfa3183ba32d6161dd14 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 12:47:26 +0100 Subject: [PATCH 250/722] Fix Subread filename to match version --- ...bread-1.5.0p1-foss-2015b.eb => Subread-1.5.0-p1-foss-2015b.eb} | 0 ...bread-1.5.0p1-foss-2016a.eb => Subread-1.5.0-p1-foss-2016a.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/Subread/{Subread-1.5.0p1-foss-2015b.eb => Subread-1.5.0-p1-foss-2015b.eb} (100%) rename easybuild/easyconfigs/s/Subread/{Subread-1.5.0p1-foss-2016a.eb => Subread-1.5.0-p1-foss-2016a.eb} (100%) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb similarity index 100% rename from easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb rename to easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb similarity index 100% rename from easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb rename to easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb -- GitLab From 476581ab23b45a00bb8d8a5bd7e94fad980ed7be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 14:42:24 +0200 Subject: [PATCH 251/722] {tools}[intel/2016a] SCOOP 0.7.1.1 w/ Python 2.7.11 --- ...reenlet-0.4.9-intel-2016a-Python-2.7.11.eb | 30 ++++++++++++++++ .../libsodium/libsodium-1.0.6-intel-2016a.eb | 20 +++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb | 28 +++++++++++++++ ...Q-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb | 28 +++++++++++++++ ...SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb | 27 ++++++++++++++ .../util-linux-2.27.1-intel-2016a.eb | 33 +++++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb | 35 +++++++++++++++++++ 7 files changed, 201 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb create mode 100644 easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..c8fb9489f2 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Greenlet' +version = '0.4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'lib/python%(pyshortver)s/site-packages/greenlet.so'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb new file mode 100644 index 0000000000..8cd02bafe0 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.6' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb new file mode 100644 index 0000000000..7d687c23fb --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb new file mode 100644 index 0000000000..3b84d83e0c --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.2.0' +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..159567d24d --- /dev/null +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'SCOOP' +version = '0.7.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/scoop/' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('Greenlet', '0.4.9', versionsuffix), + ('PyZMQ', '15.2.0', versionsuffix + '-zmq4'), +] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb new file mode 100644 index 0000000000..fa18d8bb1d --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.27.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb new file mode 100644 index 0000000000..5eeb602737 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.1.4' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.27.1'), + ('libsodium', '1.0.6'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 227f6059951a467bb27eecc6f54afda8284eef69 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 14:48:42 +0200 Subject: [PATCH 252/722] {tools}[intel/2016a] SCOOP 0.7.1.1 w/ Python 3.5.1 --- ...Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb | 30 +++++++++++++++++++ ...MQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb | 28 +++++++++++++++++ .../SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb | 27 +++++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb create mode 100644 easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..26ba01fae4 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Greenlet' +version = '0.4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'lib/python%(pyshortver)s/site-packages/greenlet.so'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb new file mode 100644 index 0000000000..40389161f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.2.0' +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..8eac309517 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'SCOOP' +version = '0.7.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/scoop/' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('Greenlet', '0.4.9', versionsuffix), + ('PyZMQ', '15.2.0', versionsuffix + '-zmq4'), +] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 31497fc893cc738df14f49f87e60e92868d78313 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:27:31 +0200 Subject: [PATCH 253/722] fix sanity check for SCOOP --- .../s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb index 8eac309517..21ced6bf47 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb @@ -20,7 +20,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s-py%(pyshortver)s.egg'], 'dirs': [], } -- GitLab From 43ac5b3c6c64f1f65f61be34acdb65097e0a2ba1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:27:48 +0200 Subject: [PATCH 254/722] fix sanity check for SCOOP --- .../s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb index 159567d24d..eb5338d376 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb @@ -20,7 +20,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s-py%(pyshortver)s.egg'], 'dirs': [], } -- GitLab From 7f64fcc96a1ceb19d3f513d26b534cf3e9b36897 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:29:01 +0200 Subject: [PATCH 255/722] fix sanity check for Greenlet --- .../g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb index 26ba01fae4..0d6aba002e 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb @@ -22,7 +22,7 @@ patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] dependencies = [('Python', '3.5.1')] sanity_check_paths = { - 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'files': ['include/python%(pyshortver)sm/greenlet/greenlet.h', 'lib/python%(pyshortver)s/site-packages/greenlet.so'], 'dirs': [], } -- GitLab From eb191c8e53282e75113408cb024eb7063c4df418 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:32:28 +0200 Subject: [PATCH 256/722] really fix sanity check for Greenlet --- .../g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb index 0d6aba002e..26eafeafb1 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb @@ -22,9 +22,8 @@ patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] dependencies = [('Python', '3.5.1')] sanity_check_paths = { - 'files': ['include/python%(pyshortver)sm/greenlet/greenlet.h', - 'lib/python%(pyshortver)s/site-packages/greenlet.so'], - 'dirs': [], + 'files': ['include/python%(pyshortver)sm/greenlet/greenlet.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'devel' -- GitLab From a671d34e8d9ffcacff21ea8076804301a2e037cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 16:24:05 +0200 Subject: [PATCH 257/722] don't hardcode .so in OpenPGM easyconfig --- easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb index 7d687c23fb..d391dfe9fd 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb @@ -21,7 +21,7 @@ configopts = '--with-pic' start_dir = 'pgm' sanity_check_paths = { - 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], 'dirs': ['include'], } -- GitLab From 9771b3cbc1b41f77c6bc468f521a821c3b7c2b1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 18:00:48 +0200 Subject: [PATCH 258/722] add zlib as explicit dep in Tk easyconfigs --- easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb | 1 + .../easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb | 1 + 29 files changed, 50 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb index 9ebfd37f5f..ff05f0890c 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb @@ -14,6 +14,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb index 5f035ccbf2..e28fd7a2dc 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb index 16d5293528..cbf7bcb4b2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb index 1415c70f4e..06a1978ba4 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.0.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb index 5c0a6ccd92..4798d6cf81 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb index f65e1a0e09..71f6f47992 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb index 25372ffd8f..11e23b0c07 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb @@ -14,6 +14,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb index 3231de70b9..8b45a8770e 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.5'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb index a79397a5f8..60130e9216 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb @@ -13,7 +13,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb index 602101704a..878cfecf53 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb index 8ff29d34a2..ac0d5ff0bc 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb index c34f24fd99..0cf00324c8 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb index 31e024fb43..aaa247a658 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb index a292e06eb8..0a860475e3 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb index cd4da6afb6..890bfc8cfe 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb index 025f5e6476..6550c8a427 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb index d841e7bd84..4762abfa09 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb index a8245c8580..684f3bddb6 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb index 05eafdb2e8..f077e32cc2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb index da82b39576..9e3efc89f0 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb index c10f179e0c..89ecb3248a 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb index 7aa028f61c..5066a5847c 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb index b3fd0e9714..9419fc66d6 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb index 7feeb34477..60f899a584 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb index 4630a6a0f4..53f70e54d2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb index 6e8ab4a8ff..85504f8688 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb index 6b8350fb20..b7e6c77202 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb index 8ada7cd405..c0f2464a6d 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb @@ -24,6 +24,7 @@ builddependencies = [ dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), (libx11, libxver), ('libXt', '1.1.5'), ('libXext', '1.3.3'), diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb index 9f46cbbff7..9eede49210 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' -- GitLab From ac6e72b23b9ffd5642a04710023df6f515bcfd9a Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Thu, 31 Mar 2016 13:05:24 +0200 Subject: [PATCH 259/722] Use `env` wherever `prebuildopts is used to set environmental variables. --- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb | 2 +- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 2 +- .../m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb | 2 +- easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb | 2 +- easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb | 2 +- .../easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb | 2 +- 24 files changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 35e328daad..c3ffc6e24a 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 6c55f76694..418f81f5f1 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -21,7 +21,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 6f9a318360..2e680c9ce3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index ef80ad6bb5..b6d6a68fc6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -21,7 +21,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index b8fa0b77ca..6858b124b1 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 9ec199023d..5378940837 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -23,7 +23,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb index 24f4ba27ec..7278d23d80 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb @@ -23,7 +23,7 @@ start_dir = 'FDS_Compilation' skipsteps = ['configure', 'install'] buildininstalldir = True -prebuildopts = 'FFLAGS="$FFLAGS -fpp"' +prebuildopts = 'env FFLAGS="$FFLAGS -fpp"' modextrapaths = {'PATH': 'FDS_Compilation'} diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 2c72b2e6f5..17513817cb 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -59,7 +59,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl" # package-config files for os dependencies are in an os specific place #preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 1a69d47441..1e7fe202e8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -57,7 +57,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 9d960059a5..43f9b4f3d2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index 73b355c719..7fe4602968 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.so', 'lib/libOSMesa.so', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 72d772f450..3ddc492ea7 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 3ee16e73ea..3fe5e0bc06 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 0cd27019ac..442c4168fe 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index a724cb0c52..82b8af7b4f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -43,7 +43,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb index 70a2816d6b..7c42ab711a 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb index 0371483898..ed80bbbf2f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 7e87cc2bd4..663c38a45e 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 9c7388d824..3df094cda8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb index 3f8c039cdb..0df4d93ef0 100644 --- a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb +++ b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb @@ -15,7 +15,7 @@ sources = ['%(name)s.v%(version)s.tar.gz'] dependencies = [('zlib', '1.2.8')] -prebuildopts = 'CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' +prebuildopts = 'env CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' buildopts = 'CC="$CC" CXX="$CXX" F77="$F77" OPTFLAG_OPT="$CFLAGS"' files_to_copy = [(['bin/Minimac3'], 'bin')] diff --git a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb index e493e1ad48..5bb00f47ad 100644 --- a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb @@ -15,7 +15,7 @@ sources = ['%(name)s.v%(version)s.tar.gz'] dependencies = [('zlib', '1.2.8')] -prebuildopts = 'CFLAGS="$CFLAGS -wd751 -L$EBROOTZLIB/lib"' +prebuildopts = 'env CFLAGS="$CFLAGS -wd751 -L$EBROOTZLIB/lib"' buildopts = 'CC="$CC" CXX="$CXX" F77="$F77" OPTFLAG_OPT="$CFLAGS"' files_to_copy = [(['bin/Minimac3'], 'bin')] diff --git a/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb index 6d97e3c57a..ea8c9d49ac 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb @@ -38,7 +38,7 @@ builddependencies = [ ] # make has problems with utf8 -prebuildopts = "LANG=C " +prebuildopts = "env LANG=C " # motif ships a broken automake and libtool preconfigopts = "rm -f libtool install-sh missing depcomp config.guess config.sub && " diff --git a/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb b/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb index 36d9829a6d..4476f0d922 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb @@ -38,7 +38,7 @@ dependencies = [ ] # make has problems with utf8 -prebuildopts = "LANG=C " +prebuildopts = "env LANG=C " # motif ships a broken automake and libtool preconfigopts = "rm -f libtool install-sh missing depcomp config.guess config.sub && " diff --git a/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb b/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb index e8dddb718d..eb272b1b70 100644 --- a/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb @@ -21,7 +21,7 @@ files_to_copy = [ dependencies = [("ncurses", "5.9")] -prebuildopts = 'DESTDIR=%(installdir)s ' +prebuildopts = 'env DESTDIR=%(installdir)s ' sanity_check_paths = { 'files': ['bin/multitail'], -- GitLab From 27192c656261f1cfaea193869f34d7afdd7a4d81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 18:28:35 +0200 Subject: [PATCH 260/722] don't hard overwrite $CPATH in prebuildopts in Mesa easyconfig files --- .../easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 2 +- .../m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 17513817cb..3f895315b2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -59,7 +59,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl" # package-config files for os dependencies are in an os specific place #preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 1e7fe202e8..592c4a1182 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -57,7 +57,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 43f9b4f3d2..2bd0ff0f94 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index 7fe4602968..a22cf02d69 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.so', 'lib/libOSMesa.so', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 3ddc492ea7..171b47710c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 3fe5e0bc06..3282ad740c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 442c4168fe..c47447d239 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index 82b8af7b4f..57483e1d4f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -43,7 +43,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb index 7c42ab711a..fa63661948 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb index ed80bbbf2f..3d2d9d7e93 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 663c38a45e..ac83c1243a 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 3df094cda8..810e10d3bb 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', -- GitLab From 15c44bd734ed1e058bd228a60cd39beab076ee84 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 17:36:49 +0100 Subject: [PATCH 261/722] Style fixes for Subread --- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb | 3 +-- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb index 4fd69f051e..4df6c05b5e 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb @@ -14,12 +14,11 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -prebuildopts = 'cd src;' +startdir = 'src &&' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] - sanity_check_paths = { 'files': ['LICENSE', 'README.txt'], 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb index 1312eb0648..f0d2074639 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb @@ -14,12 +14,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -prebuildopts = 'cd src;' +start_dir = 'src &&' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] - sanity_check_paths = { 'files': ['LICENSE', 'README.txt'], 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] -- GitLab From 7fc04b6a034430ccc672bcc4fd954b7efd947704 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 18:53:50 +0200 Subject: [PATCH 262/722] use existing libxml2 easyblock, use %(pyver)s --- .../l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb index 0237c8f83b..0df5cbd957 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -1,7 +1,6 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -18,13 +17,9 @@ sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' -pythonver = '2.7.11' -pythonshortver = '.'.join(pythonver.split('.')[:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.11'), ] moduleclass = 'lib' -- GitLab From 0d6511bd1d3ba7dcafa852dc033de9aff737a052 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 18:05:34 +0100 Subject: [PATCH 263/722] Use new-style pyver and make sanity_check paths more specific --- .../r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb index 4fc2b27c34..a177369637 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb @@ -6,6 +6,7 @@ easyblock = 'PythonPackage' name = 'RSeQC' version = '2.6.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://rseqc.sourceforge.net/' description = """RSeQC provides a number of useful modules that can @@ -20,21 +21,17 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCE_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] -python = 'Python' -pyver = '2.7.10' -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ ('R', '3.2.3'), - (python, pyver), - ('numpy', '1.10.1', versionsuffix), + ('Python', '2.7.10'), ] runtest = "python setup.py test" sanity_check_paths = { - 'files': [], - 'dirs': ["bin", "lib"] + 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', + 'bin/split_paired_bam.py'], + 'dirs': ['lib'] } options = {'modulename': 'qcmodule'} -- GitLab From e991040ec94fd7b22bab054ff840999434975cd3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 19:06:51 +0200 Subject: [PATCH 264/722] consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs --- easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 2 +- 27 files changed, 27 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb index 31c851b3d9..8398e40d06 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.06'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb index 3010711346..b84761b602 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb index b62284872a..b4bb4c955d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb index c2e9e52426..5df1dda5a3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb index 90c7eb9017..f406268a87 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb index a79d153988..560606e07a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb index 372d1c346d..00b1eb05a8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb index 0fa72c61c9..a939e01023 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb index 89984f9baf..64c98aad33 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb index 52fc84e052..745063ebad 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb index e856a3fd43..a95ac9f601 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb index e2764250bf..134d181212 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb index ad83091b2b..25f9aacace 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb index e83b261924..5ca90d16a7 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb index 94ec58056b..4abe05a74f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb index 411820a76b..f58173164e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb index b66775c7a6..6a7048dcf1 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb index 42808d7b77..aa806c1087 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb index 3b4187acd1..304b160de5 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb index e8d95f1f54..46c1b375cb 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb index 68b3d851f6..0289e6c40e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '7.1.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb index d6a8a6e705..857e1b9ffc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb index f842bdc90a..a805266216 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb index 292da57c7e..6746b4b3a4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb index 519be6b6b3..4472772492 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb index 37a6837b2b..104ad6a3bd 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel-para', 'version': '2014.12'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 3f396ce26b..2bc8d9c022 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 2469d572c2a76c37fc5fb46c174678e48b6c85c8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 18:32:03 +0100 Subject: [PATCH 265/722] Add R suffix and fix sanity_check style --- ....10.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/r/RSeQC/{RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb} (89%) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb similarity index 89% rename from easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb index a177369637..58d91e5c53 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb @@ -7,6 +7,7 @@ easyblock = 'PythonPackage' name = 'RSeQC' version = '2.6.3' versionsuffix = '-Python-%(pyver)s' +versionsuffix += '-R-%(rver)s' homepage = 'http://rseqc.sourceforge.net/' description = """RSeQC provides a number of useful modules that can @@ -29,8 +30,7 @@ dependencies = [ runtest = "python setup.py test" sanity_check_paths = { - 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', - 'bin/split_paired_bam.py'], + 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', 'bin/split_paired_bam.py'], 'dirs': ['lib'] } -- GitLab From 6027c4ad03cf95b635270fa365e376735c183426 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 31 Mar 2016 13:47:56 -0500 Subject: [PATCH 266/722] Renamed Easyconfig file from gtool-0.7.5-linux_x86_64.eb to gtool-0.7.5_linux_x86_64.eb --- .../{gtool-0.7.5-linux_x86_64.eb => gtool-0.7.5_linux_x86_64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/gtool/{gtool-0.7.5-linux_x86_64.eb => gtool-0.7.5_linux_x86_64.eb} (100%) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb similarity index 100% rename from easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb rename to easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb -- GitLab From 61839ae12b5c739ec3e36b4ee971cd5e4da2d3f8 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 31 Mar 2016 14:18:10 -0500 Subject: [PATCH 267/722] Renamed Easyconfig file from shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb to shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb --- ...-linux_x86_64.eb => shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/shapeit/{shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb => shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb} (100%) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb rename to easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb -- GitLab From 4df62bb5e637f584d3ebffb56b2fd25d40a94b2b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 22:11:56 +0100 Subject: [PATCH 268/722] Use start_dir, not startdir for Subread --- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb index 4df6c05b5e..5192855877 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -startdir = 'src &&' +start_dir = 'src &&' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] -- GitLab From 6dfc122e053950dd94d862cb80be20a6797e4e12 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 22:35:29 +0100 Subject: [PATCH 269/722] Style cleanup for versionsuffix --- .../r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb index 58d91e5c53..d3a31d723c 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb @@ -6,8 +6,7 @@ easyblock = 'PythonPackage' name = 'RSeQC' version = '2.6.3' -versionsuffix = '-Python-%(pyver)s' -versionsuffix += '-R-%(rver)s' +versionsuffix = '-Python-%(pyver)s-R-%(rver)s' homepage = 'http://rseqc.sourceforge.net/' description = """RSeQC provides a number of useful modules that can -- GitLab From 37491f387e1a294625a7d71fa72bd06065326dba Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 1 Apr 2016 10:10:53 +0100 Subject: [PATCH 270/722] Fix start_dir --- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb | 2 +- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb index 5192855877..612c514399 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -start_dir = 'src &&' +start_dir = 'src' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb index f0d2074639..e525a015c8 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -start_dir = 'src &&' +start_dir = 'src' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] -- GitLab From 2e4f5401e6f65f307bbfced75186d8a0f43aba91 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 1 Apr 2016 11:00:50 -0500 Subject: [PATCH 271/722] Converting from 'Binaries' Easyblock to 'Tarball'. --- easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb index 6d1dad133e..bc3ceffb75 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Binary" +easyblock = "Tarball" name = 'gtool' version = '0.7.5' @@ -16,10 +16,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] sources = ['gtool_v%(version)s_x86_64.tgz'] -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " -install_cmd += "cp -a %(builddir)s/* %(installdir)s" - sanity_check_paths = { 'files': ["gtool", "LICENCE"], 'dirs': ["example"] -- GitLab From 163189467710769bcb3fc8785cfc0bc719ab8ac1 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 1 Apr 2016 11:07:32 -0500 Subject: [PATCH 272/722] Converting from 'Binaries' Easyblock to 'Tarball'. --- .../s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb index 7441bd58af..75a894a8c8 100644 --- a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb +++ b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Binary" +easyblock = "Tarball" name = 'shapeit' version = '2.r837.GLIBCv2.12' @@ -16,10 +16,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] sources = ['shapeit.v%(version)s.Linux.static.tgz'] -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "tar xzvf shapeit.v%(version)s.Linux.static.tgz && HOME=%(builddir)s && " -install_cmd += "cp -a %(builddir)s/* %(installdir)s" - sanity_check_paths = { 'files': ["bin/shapeit", "LICENCE"], 'dirs': ["example"] -- GitLab From 53eccaea377809af2cf69d87b18ef86843a6cf79 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 00:05:44 -0700 Subject: [PATCH 273/722] add easyconfig for LAME MP3 encoder --- .../l/LAME/LAME-3.99.5-foss-2015a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb new file mode 100644 index 0000000000..8ce773805a --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.99.5' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] + +dependencies = [('ncurses', '5.9')] + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.so'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From d07bf5d6c4a52bb9f65d5d8add7c300ce05b084d Mon Sep 17 00:00:00 2001 From: jgp Date: Sat, 2 Apr 2016 09:21:03 +0200 Subject: [PATCH 274/722] qt/486 for dummy toolchain --- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb new file mode 100644 index 0000000000..5c83d337b8 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -0,0 +1,15 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] +sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] + +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' +platform = 'linux-g++-64' + +moduleclass = 'devel' -- GitLab From 686957e8a63d021e32cc88fe2a96e09e131651e2 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 00:42:51 -0700 Subject: [PATCH 275/722] Pygments: fix homepage URL and description --- .../p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb | 4 ++-- .../p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb index 103bb38998..dc2b7c311c 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb @@ -3,8 +3,8 @@ easyblock = 'PythonPackage' name = 'Pygments' version = '2.0.2' -homepage = 'https://pypi.python.org/pypi/requests/2.6.0' -description = """Python http for humans""" +homepage = 'http://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb index 06251d7872..45a6907cbe 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -3,8 +3,8 @@ easyblock = 'PythonPackage' name = 'Pygments' version = '2.0.2' -homepage = 'https://pypi.python.org/pypi/requests/2.6.0' -description = """Python http for humans""" +homepage = 'http://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" toolchain = {'name': 'intel', 'version': '2015a'} -- GitLab From 9e88f53c5f8c8aa7540c08f84b5c96a77d720fd1 Mon Sep 17 00:00:00 2001 From: jgp Date: Sat, 2 Apr 2016 14:14:43 +0200 Subject: [PATCH 276/722] fixing line max length --- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb index 5c83d337b8..48c0604f80 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -9,7 +9,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] -configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' +configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' platform = 'linux-g++-64' moduleclass = 'devel' -- GitLab From 79a0eb02eaac79c6058e84ca25a9326a731c1970 Mon Sep 17 00:00:00 2001 From: jgp Date: Sat, 2 Apr 2016 14:29:52 +0200 Subject: [PATCH 277/722] adding -no-webkit for redhat builds --- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb index 48c0604f80..eacf9a8384 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -9,8 +9,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] -configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' -configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' +configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite -no-webkit' platform = 'linux-g++-64' moduleclass = 'devel' -- GitLab From 05a5e0a091c4191a14cac7cf03367874b7e20eae Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 20:53:00 -0700 Subject: [PATCH 278/722] add easyconfig for FLAC audio codec --- .../f/FLAC/FLAC-1.3.1-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb new file mode 100644 index 0000000000..72f2e62fcc --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.3.1' + +homepage = 'https://xiph.org/flac/' +description = """Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://downloads.xiph.org/releases/flac/'] + +sanity_check_paths = { + 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.so'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 28b3cea3b180c4b84704914f72a04857aaa980f5 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 21:08:27 -0700 Subject: [PATCH 279/722] add easyconfig for SoX (a Torch7 dependency) --- .../s/SoX/SoX-14.4.2-foss-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb new file mode 100644 index 0000000000..8228308a17 --- /dev/null +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'SoX' +version = '14.4.2' + +homepage = 'http://http://sox.sourceforge.net/' +description = """Sound eXchange, the Swiss Army knife of audio manipulation""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sourceforge.net/projects/sox/files/sox/%(version)s'] + +# These are not strictly mandatory but add flac and mp3 support to SoX +dependencies = [ + ('FLAC', '1.3.1'), + ('LAME', '3.99.5') +] + +sanity_check_paths = { + 'files': ['bin/sox', 'include/sox.h', 'lib/libsox.so'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From f42683f08dedc4e4c9980e0d116ef92403cbc805 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 Apr 2016 14:01:34 +0200 Subject: [PATCH 280/722] add easyconfig scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb --- ...-learn-0.17.1-intel-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..50d044b41c --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.17.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 65c8245f61d91344b4965fe2f35a153fee92de78 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 09:51:25 -0700 Subject: [PATCH 281/722] FLAC: use SHLIB_EXT rather than hardcoding .so --- easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb index 72f2e62fcc..509bb248c0 100644 --- a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://downloads.xiph.org/releases/flac/'] sanity_check_paths = { - 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.so'], + 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From dddf87803d9b9f070568fdefa07f7a2325437c23 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 09:54:55 -0700 Subject: [PATCH 282/722] Pygments: keep lines under 120 characters --- .../p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb | 3 ++- .../p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb index dc2b7c311c..bfe92c90eb 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb @@ -4,7 +4,8 @@ name = 'Pygments' version = '2.0.2' homepage = 'http://pygments.org/' -description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb index 45a6907cbe..3c3f9ad92d 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -4,7 +4,8 @@ name = 'Pygments' version = '2.0.2' homepage = 'http://pygments.org/' -description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" toolchain = {'name': 'intel', 'version': '2015a'} -- GitLab From c4186634b8ced2d454d53bad348efcde85150ff3 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 10:11:01 -0700 Subject: [PATCH 283/722] use SHLIB_EXT rather than .so --- easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb index 8ce773805a..a1da0d2c90 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb @@ -23,7 +23,7 @@ dependencies = [('ncurses', '5.9')] configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " sanity_check_paths = { - 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.so'], + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From 4505dcb1a2b2ccb0274b3e7dc991244ca376ec8e Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 10:20:21 -0700 Subject: [PATCH 284/722] SoX: use SHLIB_EXT rather than hardcoding .so --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb index 8228308a17..a71ba0bca6 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb @@ -24,7 +24,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/sox', 'include/sox.h', 'lib/libsox.so'], + 'files': ['bin/sox', 'include/sox.h', 'lib/libsox.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From a9481ca6559314b4ddf261a8030df7426a7e3251 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Apr 2016 10:57:07 +0200 Subject: [PATCH 285/722] add binutils as build dep for FLAC, also run tests --- easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb index 509bb248c0..76be36ffc6 100644 --- a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -17,6 +17,11 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://downloads.xiph.org/releases/flac/'] +# use of assembly routines requires a recent binutils +builddependencies = [('binutils', '2.25', '', ('GCC', '4.9.2'))] + +runtest = 'check' + sanity_check_paths = { 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.%s' % SHLIB_EXT], 'dirs': [], -- GitLab From e20aeaca67693bf5be63cd89953e98b9071642dd Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 10:03:55 -0500 Subject: [PATCH 286/722] Changed software name to uppercase (to match the official software name) --- easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb index bc3ceffb75..8b1697e3af 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -4,12 +4,12 @@ easyblock = "Tarball" -name = 'gtool' +name = 'GTOOL' version = '0.7.5' -versionsuffix = '_linux_x86_64' homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' -description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ +description = """ GTOOL is a program for transforming sets of genotype data for use with +the programs SNPTEST and IMPUTE. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From b9707b6147bbd5662971c333ff5a371bf7624483 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 10:13:29 -0500 Subject: [PATCH 287/722] Changed the name to SHAPEIT(uppercase), to match the official software name as well as added GLIBCv2.12 part as a versionsuffix --- .../shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb index 75a894a8c8..f2424bbea4 100644 --- a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb +++ b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb @@ -4,17 +4,18 @@ easyblock = "Tarball" -name = 'shapeit' -version = '2.r837.GLIBCv2.12' -versionsuffix = '_linux_x86_64' +name = 'SHAPEIT' +version = '2.r837' +versionsuffix = '.GLIBCv2.12' homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html' -description = """ SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. """ +description = """SHAPEIT is a fast and accurate method for estimation of +haplotypes (aka phasing) from genotype or sequencing data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] -sources = ['shapeit.v%(version)s.Linux.static.tgz'] +sources = ['shapeit.v%(version)s%(versionsuffix)s.Linux.static.tgz'] sanity_check_paths = { 'files': ["bin/shapeit", "LICENCE"], -- GitLab From acd19f1aef37e3efbdc6afb2aa3393f73d6a6e5e Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 10:57:50 -0500 Subject: [PATCH 288/722] Renamed the Easyconfig file --- .../g/{gtool/gtool-0.7.5_linux_x86_64.eb => GTOOL-0.7.5.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{gtool/gtool-0.7.5_linux_x86_64.eb => GTOOL-0.7.5.eb} (100%) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/GTOOL-0.7.5.eb similarity index 100% rename from easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb rename to easybuild/easyconfigs/g/GTOOL-0.7.5.eb -- GitLab From e11bdeb3d103cd2b7bfd0538ba674537d47fd89c Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:06:12 -0500 Subject: [PATCH 289/722] Renamed the Easyconfig file --- easybuild/easyconfigs/g/{ => gtool}/GTOOL-0.7.5.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{ => gtool}/GTOOL-0.7.5.eb (100%) diff --git a/easybuild/easyconfigs/g/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb similarity index 100% rename from easybuild/easyconfigs/g/GTOOL-0.7.5.eb rename to easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb -- GitLab From 4f08e6223419bd817ec1345de6bf367d0bdccac7 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:10:38 -0500 Subject: [PATCH 290/722] Renamed the Easyconfig file --- ...37.GLIBCv2.12_linux_x86_64.eb => SHAPEIT-2.r837.GLIBCv2.12.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/shapeit/{shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb => SHAPEIT-2.r837.GLIBCv2.12.eb} (100%) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb rename to easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb -- GitLab From d21d922f81159e6d35ae23969d32b56797458ac4 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:40:26 -0500 Subject: [PATCH 291/722] Renamed the directory from 'gtool' to 'GTOOL' --- easybuild/easyconfigs/g/{gtool => GTOOL}/GTOOL-0.7.5.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{gtool => GTOOL}/GTOOL-0.7.5.eb (100%) diff --git a/easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb similarity index 100% rename from easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb rename to easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb -- GitLab From 03d799432b512447956e6f35f56370817d04b817 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:42:44 -0500 Subject: [PATCH 292/722] Renamed the directory from 'shapeit' to 'SHAPEIT' --- .../s/{shapeit => SHAPEIT}/SHAPEIT-2.r837.GLIBCv2.12.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/{shapeit => SHAPEIT}/SHAPEIT-2.r837.GLIBCv2.12.eb (100%) diff --git a/easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb rename to easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb -- GitLab From 64c78cbac01a04a0771040e2cf3ccfa69aa16c14 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 12:44:17 -0500 Subject: [PATCH 293/722] Adding 'modextrapaths' parameter to include the root directory in the PATH variable --- easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb index 8b1697e3af..69e22e6cab 100644 --- a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb +++ b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb @@ -16,6 +16,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] sources = ['gtool_v%(version)s_x86_64.tgz'] +modextrapaths = {'PATH': ''} + sanity_check_paths = { 'files': ["gtool", "LICENCE"], 'dirs': ["example"] -- GitLab From 6057e0642b6b7e61c5e68a69c1709d485e17a6c9 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:44:50 -0400 Subject: [PATCH 294/722] libxcb-1.11.1 easyconfig for foss-2016a --- .../l/libxcb/libxcb-1.11.1-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb new file mode 100644 index 0000000000..b12be025db --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('pkg-config', '0.29'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), + ('xcb-proto', '1.11', '', True), + ('libpthread-stubs', '0.3'), + +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 3c13fbcd743487e7e4fd7ecc7faa633e07d827d2 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:53:45 -0400 Subject: [PATCH 295/722] xproto-7.0.28 easyconfig for foss-2016a --- .../x/xproto/xproto-7.0.28-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb new file mode 100644 index 0000000000..3e787177f0 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 76dbf608ede3b5ec4fc28fb94e93b9ce633e50ad Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:56:17 -0400 Subject: [PATCH 296/722] libpthread-stubs-0.3 easyconfig for foss-2016a --- .../libpthread-stubs-0.3-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb new file mode 100644 index 0000000000..fcb767cfdb --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From d9ec15efee75c4133c9b4476d5eca278ee28bfb5 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:59:14 -0400 Subject: [PATCH 297/722] libXau-1.0.8 easyconfig for foss-2016a --- .../l/libXau/libXau-1.0.8-foss-2016a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..b6f23c9a07 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('pkg-config', '0.29'), +] + +dependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 0ee9e5f553a8df087774e50b56875a009b0c96b9 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 16:00:39 -0400 Subject: [PATCH 298/722] libXdmcp-1.1.2 easyconfig for foss-2016a --- .../l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..9e90ec9775 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('pkg-config', '0.29') +] + +dependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 76339fa83cdd28958c5dd3e44282321dffaa260c Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 16:01:47 -0400 Subject: [PATCH 299/722] pkg-config-0.29 easyconfig for foss-2016a --- .../pkg-config/pkg-config-0.29-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb new file mode 100644 index 0000000000..2796515752 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 508d9ac2b09b1bffc86709993300f41fee471478 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 5 Apr 2016 15:23:39 -0500 Subject: [PATCH 300/722] Changing the file name and the folder name containing it. --- .../MRIcron-06_22_15.eb} | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/m/{mricron/mricron-062215-linux_x86_64.eb => MRIcron/MRIcron-06_22_15.eb} (60%) diff --git a/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb similarity index 60% rename from easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb rename to easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index a7fb738545..097d50c5b6 100644 --- a/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -4,20 +4,22 @@ easyblock = "Binary" -name = 'mricron' -version = '062215' -versionsuffix = '_linux_x86_64' +name = 'MRIcron' +version = '06_22_15' homepage = 'http://www.mccauslandcenter.sc.edu/mricro/mricron/' -description = """ MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering. """ +description = """ MRIcron allows viewing of medical images. It +includes tools to complement SPM and FSL. Native format is NIFTI +but includes a conversion program (see dcm2nii) for converting DICOM images. +Features layers, ROIs, and volume rendering. """ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] sources = ['lx.zip'] -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "unzip lx.zip && HOME=%(builddir)s && " +# Following commands are used to unzip the files and copy the content to install directory +install_cmd = "unzip lx.zip &&" install_cmd += "cp -a %(builddir)s/* %(installdir)s" sanity_check_paths = { -- GitLab From 030b70a2a075c3b29af339d5210a6569e2d14def Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 6 Apr 2016 11:33:39 +0200 Subject: [PATCH 301/722] {vis}[intel-2016a] Pillow 3.2.0 (REVIEW) --- .../Pillow-3.2.0-intel-2016a-Python-2.7.11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..bc1187561f --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '3.2.0' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.11' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('libjpeg-turbo', '1.4.2'), + ('zlib', '1.2.8'), + ('LibTIFF', '4.0.6'), + ('freetype', '2.6.2'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' -- GitLab From e53d9aea980e8a51a012176937fea91cb3cf0255 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 6 Apr 2016 15:41:33 +0200 Subject: [PATCH 302/722] Libxslt-1.1.28 for foss-2016a --- .../l/libxslt/libxslt-1.1.28-foss-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb new file mode 100644 index 0000000000..63c3fa7e2d --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), +] + +moduleclass = 'lib' \ No newline at end of file -- GitLab From 2f2d57ae191b8c71b2dd9015965a617f608ddb30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Apr 2016 18:01:14 +0200 Subject: [PATCH 303/722] consistently use XORG_LIB_SOURCE constant --- easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb | 2 +- .../l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb | 2 +- .../l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb | 2 +- 34 files changed, 34 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb index bb3839e6a6..ff2702cd71 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.4'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb index 407ce4845d..b63222e9d8 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb index 0fb685525a..1bd7511944 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb index d28d3a6e76..2f28c257c5 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb index 0038b41047..bd5ecc8bcd 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb index a15bba69ef..30a7625681 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.8'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb index 580ce7f28a..a8d0c1fc55 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb index 2a2391d847..c3a28914e6 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb index 641ea44476..503006a89b 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb index b34ef0db33..1bab5701fe 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb index 3522b7de99..3a034255d6 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X11 client-side library""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] pythonversion = '-Python-2.7.8' builddependencies = [ diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb index 8694ab5ad2..96ec24e1fc 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb index 2e88286d07..934e207665 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb index f1bc2bfb36..bd0254a335 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb index 22bf8016cf..afa4166c18 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.26'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb index 408dc4aede..1accebb77f 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb index 9304d0fc79..dafc84e463 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb index 243dbd6f22..8003dc09d5 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb index 735a0391ab..efb7a8e46c 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.26'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb index c12e65e6e8..20f0072ce3 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb index 9233da540e..395760652d 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb index cc513f2315..599620e265 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb index 79416debdd..0912eb0311 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb index 93de3908f0..1639916a6f 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb index 24fc239d5e..6ec7ecf45d 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb index 1eeae06c66..b642948a1b 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libX11', '1.6.1'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb index 9ce9ef676f..388076a498 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb index f5d31320dd..e0c74eaaa7 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb index fea0b330b9..59f66ccd07 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb index c076690abe..3b9f118dec 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb index 23544e2ee3..7c257d0a2f 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb index 93ffb79a95..3751e0a221 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 3e89327b58..2b4eff3bde 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb index 6f79135801..4646632358 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libSM', '1.2.1'), -- GitLab From 1e6a202f0f1415b190d434c94c74464ddccbfc9f Mon Sep 17 00:00:00 2001 From: jrbosch Date: Wed, 6 Apr 2016 12:45:43 -0400 Subject: [PATCH 304/722] Update libXdmcp-1.1.2-foss-2016a.eb --- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb index bbe5e2fcc0..dcd4997f9b 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] builddependencies = [ - ('pkg-config', '0.29') + ('pkg-config', '0.29'), ('xproto', '7.0.28'), ] -- GitLab From b9dfd342150f7b28e69e6c96746ab2f2537a5b8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Apr 2016 19:12:21 +0200 Subject: [PATCH 305/722] consistently use XORG_*_SOURCE constants --- .../easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb | 2 +- .../easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb | 2 +- easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb | 2 +- .../easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb | 2 +- .../easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb | 2 +- easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb | 2 +- .../easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb | 2 +- 95 files changed, 95 insertions(+), 95 deletions(-) diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb index 88fa55c14d..1deb262347 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb index 80e72c01e5..574d6d02de 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb index c52db08f49..15154dbbea 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb index 06e3d71fba..4df2be2be9 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb index 5d430a5301..8b11789fca 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb index 3fe841d973..fd373c373a 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb index 33951308af..f26ed2df7a 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb index 0719ec51f4..8e577e277b 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb index 6c5ce99387..47f2d3c961 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb index 5c83a62b97..062cfdbcf8 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb index 5b1c1517ba..9c00b32506 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb index f9c5e14a8e..4282ea773f 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb index 06b846c04c..037260e492 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb index 42dc60dd5e..aebc924b14 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb index 8b99a901c9..cb35b32223 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb index 6ccc91bb75..c92de947ba 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb index 2566876879..1f4bad7112 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb index 46b9bdb324..8a7667c002 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb index 4eb87a66ef..b28bfab5ef 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb index a1f9a0b9d2..191cd512ed 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb index c26a1ac08a..5dd250fddb 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb index 3297e8dea0..ce9480d3aa 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb index 1e1be175b1..475b25485e 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb index 56a7e864e0..7ae3e0efff 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb index 75a9c42cf7..9931bbca58 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb index 804a25ce18..19917b0ef7 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb index e307d5deb4..eb95b2f34a 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb index 0437a042db..d652aba387 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb index be4171cde7..cad6b846e6 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb index 1a5db1eefa..b26cb20222 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb index 66fc05b6d4..6a557da522 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb index 21d5d376d5..512fcad715 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb index 83bc32fc03..00ad73c8ec 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb index 323816dd0b..f40968ca7a 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb index 7482053f6f..30967e9fe4 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb index e54e5f74c9..7e3ad5f572 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb index 3790a57f15..ee1d8ab5ad 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb index 664996727e..48cbc77814 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb index 31cb837d0f..2393fe61dc 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb index 2d16cb0b13..295d7b8f94 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb index bca5ddd7ca..86f8eb23de 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb index 050b2bda55..a2add0de30 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb index 62923f260f..13dbd2eb08 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb index d692faf393..9a5a48c480 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb index 29d6a6987a..e5d229774c 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index fc57003279..ce3e6d964e 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb index dacbb816a7..3f72d96af4 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb index db2b6fad94..83069f50b6 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb index ae82f50061..bd1a547705 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb index 0e5bfb142c..38e0bbe3cc 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb index cb2cc76a3b..87f1456d12 100644 --- a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = "Xrandr protocol and ancillary headers" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb index 278cc7bbbf..563fbfcbf2 100644 --- a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb @@ -9,7 +9,7 @@ description = "Xrandr protocol and ancillary headers" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb index 3119cd29b7..a354245bf6 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb index 48199d0511..9f19fc4dfc 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb index c363620cb6..c2eb005cc6 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb index 9d7f0c2a91..c0cb8f56f1 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb index 87042e0e65..59a4298687 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb index b16c201ac1..20a477feb6 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb index 37b516e535..c3ac221b11 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb index 93be023dae..9e6fad7729 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb index 7edd725bb8..6dfd84dd09 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb index 38732656c2..23a639e880 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb index f7d2e42a4b..c294b4f211 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb index 7c6cc82582..4cb4a74155 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb index 222c1cb8a9..c125fc2989 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb index f8d28a6517..658fd35838 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb index 7e5dd65346..a2085627e9 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb index e73a8f9515..6edad56122 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb index 0f74426405..bd75285755 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb index bceed61321..3876294b7f 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb index 9bc6335cdf..53735a84e4 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb index 1800fbf094..beda89b5c6 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb index eb7322e162..82aff3127f 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb index 6156597f8b..4a87699495 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb index 96189817b0..91c591e727 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb index d2b93b5852..c2246d9293 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb index af65fa2a9d..08ca1e412b 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb index b0ee431324..883ec594b7 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb index 797b75e5e7..e582ff06dd 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb index e96e89759a..7e6eb92e97 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb index d198aa80e4..892ed9f5bd 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb index f6c2e0c627..572e38002b 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb index 241268e4a6..6eb06bc7d4 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb index ab202e5075..5054d70df3 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb index e0f4abf144..ddf767b605 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb index 884e64e8dd..06bdb8bc21 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb index 8f17ba5d45..7d12c7f86a 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb index bdb6d9e8c7..76cc9f4a7a 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb index 74b305ce8c..1caa382ace 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb index 4ec0e6221a..4d66b00ecb 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb index f9bd7118c8..a0292fbf8e 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb index 3e787177f0..2a47f2490b 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb index 2591e436f9..8dab7213fb 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb index d3de936da4..6722798efb 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb index 1d3df458a7..9de353786c 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', -- GitLab From c025b26559a8de6353a6e2f64b8a16413b2f1900 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 13:06:53 -0500 Subject: [PATCH 306/722] Adhering to the 120 characters per line standard for the description variable --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 097d50c5b6..64d81e0783 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Binary" +easyblock = "PackedBinary" name = 'MRIcron' version = '06_22_15' @@ -19,8 +19,8 @@ source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] sources = ['lx.zip'] # Following commands are used to unzip the files and copy the content to install directory -install_cmd = "unzip lx.zip &&" -install_cmd += "cp -a %(builddir)s/* %(installdir)s" +#install_cmd = "unzip lx.zip &&" +#install_cmd += "cp -a %(builddir)s/* %(installdir)s" sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], -- GitLab From 8be21fa9d9b4d44c566d83c7b8e48cf187d7f4f5 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 13:31:56 -0500 Subject: [PATCH 307/722] Removing source_url and adding a comment detailing how to download zip'd files manually from the website --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 64d81e0783..a984af8d3b 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -15,12 +15,10 @@ Features layers, ROIs, and volume rendering. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] -sources = ['lx.zip'] - -# Following commands are used to unzip the files and copy the content to install directory -#install_cmd = "unzip lx.zip &&" -#install_cmd += "cp -a %(builddir)s/* %(installdir)s" +# Automatic Download doesn't work for this software sice you need to accept their +# license, so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ +# and place it in a folder where Easybuild can see it. +sources = [SOURCE.ZIP] sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], -- GitLab From d45ee07c957fb86c3a3794ee2ee8f085ccbf68ec Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 13:57:55 -0500 Subject: [PATCH 308/722] Corrected some spell errors --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index a984af8d3b..4c0655294e 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -15,8 +15,8 @@ Features layers, ROIs, and volume rendering. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -# Automatic Download doesn't work for this software sice you need to accept their -# license, so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ +# Automatic Download doesn't work for this software as you need to accept their license, +# so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ # and place it in a folder where Easybuild can see it. sources = [SOURCE.ZIP] -- GitLab From 4c0b59ae9650f557c12569e0085e22f6ec14e1e2 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 14:34:11 -0500 Subject: [PATCH 309/722] Adding the source file to the Easyconfig file --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 4c0655294e..daea20393e 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Automatic Download doesn't work for this software as you need to accept their license, # so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ # and place it in a folder where Easybuild can see it. -sources = [SOURCE.ZIP] +sources = ['lx.zip'] sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], -- GitLab From d97b12f986e603dac7e20078dd6db73d79ac709d Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 15:06:42 -0500 Subject: [PATCH 310/722] Adding the md5 checksum value for the source --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index daea20393e..69196eb784 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -20,6 +20,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # and place it in a folder where Easybuild can see it. sources = ['lx.zip'] +checksums = ['a2d8b1c053384220953f6b670d0fd4df'] + sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], 'dirs': ["example", "lut", "templates"] -- GitLab From 29f2c6b09b5e6b7d871d0da26aab6597c5c52163 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 18:05:56 -0400 Subject: [PATCH 311/722] libXrandr-1.5.0 easyconfig for foss-2016a --- .../l/libXrandr/libXrandr-1.5.0-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..b6614e79e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXrandr' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Resize, Rotate and Reflection extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('randrproto', '1.5.0'), + ('renderproto', '0.11'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrandr.%s' % SHLIB_EXT, 'lib/libXrandr.a'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From a7a61c9d0568c5d4f59df08abb5aae85f3def8f4 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 18:08:32 -0400 Subject: [PATCH 312/722] randrproto-1.5.0 easyconfig for foss-2016a --- .../randrproto/randrproto-1.5.0-foss-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..d480848616 --- /dev/null +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'randrproto' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrandr protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 44cf756826c8e52b397447b030e627360e7c5bdf Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:38:57 -0400 Subject: [PATCH 313/722] libXi-1.7.6 for foss-2016a toolchain --- .../l/libXi/libXi-1.7.6-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb new file mode 100644 index 0000000000..bd92d68db6 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' +name = 'libXi' +version = '1.7.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('inputproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From a5dd9bfb4552cf157384fbccf9b9538e771453f7 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:39:56 -0400 Subject: [PATCH 314/722] libXfixes-5.0.1 for foss-2016a toolchain --- .../l/libXfixes/libXfixes-5.0.1-foss-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb new file mode 100644 index 0000000000..aa11951f76 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From fd70a1bdd1a84da2729aa341abe5e8262512e767 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:41:19 -0400 Subject: [PATCH 315/722] xorg-macros-1.19.0 for foss-2016a toolchain --- .../xorg-macros-1.19.0-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 285276c385c90279c966915beba4bb24fbc1aae1 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:44:31 -0400 Subject: [PATCH 316/722] fixesproto-5.0 for foss-2016a toolchain --- .../f/fixesproto/fixesproto-5.0-foss-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb new file mode 100644 index 0000000000..b04efa3b3a --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From 03e17713072089963a0bceb1a92e343f650ef664 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Thu, 7 Apr 2016 00:21:05 -0400 Subject: [PATCH 317/722] libGLU for foss-2016a toolchain --- .../l/libGLU/libGLU-9.0.0-foss-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb new file mode 100644 index 0000000000..087bd589cb --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '11.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 6db2fe08a4d22e3e21471bca3ae1eb74e3bc437d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 7 Apr 2016 09:37:09 +0200 Subject: [PATCH 318/722] use of %(pyver)s --- .../p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb index bc1187561f..e08e25c6bb 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'Pillow' version = '3.2.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. @@ -12,12 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = 'Python' -pyver = '2.7.11' -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.11'), ('libjpeg-turbo', '1.4.2'), ('zlib', '1.2.8'), ('LibTIFF', '4.0.6'), -- GitLab From f5cca74c3cae5b9e3e51677a37cc33fd0e25993d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:02:48 +0200 Subject: [PATCH 319/722] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig GLib-2.47.5-foss-2016a.eb, modify easyconfig freetype-2.6.2-foss-2016a.eb, modify easyconfig pixman-0.34.0-foss-2016a.eb, modify easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig libX11-1.6.3-foss-2016a.eb, add easyconfig libxcb-1.11.1-foss-2016a.eb, add easyconfig libXrender-0.9.9-foss-2016a.eb, add easyconfig libXext-1.3.3-foss-2016a.eb, add easyconfig renderproto-0.11-foss-2016a.eb, add easyconfig xextproto-7.3.0-foss-2016a.eb, add easyconfig xproto-7.0.28-foss-2016a.eb, add easyconfig libffi-3.2.1-foss-2016a.eb, add easyconfig gettext-0.19.7-foss-2016a.eb, add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb, add easyconfig PCRE-8.38-foss-2016a.eb, add easyconfig inputproto-2.3.1-foss-2016a.eb, add easyconfig libpthread-stubs-0.3-foss-2016a.eb, add easyconfig kbproto-1.0.7-foss-2016a.eb, add easyconfig xtrans-1.3.5-foss-2016a.eb, add easyconfig xorg-macros-1.19.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 30 ++++++++++++++- .../g/GLib/GLib-2.47.5-foss-2016a.eb | 33 +++++++++++++++++ .../g/gettext/gettext-0.19.7-foss-2016a.eb | 23 ++++++++++++ .../inputproto/inputproto-2.3.1-foss-2016a.eb | 19 ++++++++++ .../k/kbproto/kbproto-1.0.7-foss-2016a.eb | 19 ++++++++++ .../l/libX11/libX11-1.6.3-foss-2016a.eb | 37 +++++++++++++++++++ .../l/libXext/libXext-1.3.3-foss-2016a.eb | 34 +++++++++++++++++ .../libXrender/libXrender-0.9.9-foss-2016a.eb | 32 ++++++++++++++++ .../l/libffi/libffi-3.2.1-foss-2016a.eb | 23 ++++++++++++ .../libpthread-stubs-0.3-foss-2016a.eb | 20 ++++++++++ .../l/libxcb/libxcb-1.11.1-foss-2016a.eb | 33 +++++++++++++++++ .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++ .../p/PCRE/PCRE-8.38-foss-2016a.eb | 20 ++++++++++ .../renderproto-0.11-foss-2016a.eb | 20 ++++++++++ .../x/xextproto/xextproto-7.3.0-foss-2016a.eb | 24 ++++++++++++ .../xorg-macros-1.19.0-foss-2016a.eb | 22 +++++++++++ .../x/xproto/xproto-7.0.28-foss-2016a.eb | 23 ++++++++++++ .../x/xtrans/xtrans-1.3.5-foss-2016a.eb | 22 +++++++++++ 18 files changed, 462 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index 4afe79dcce..ab395e2001 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = "cairo" +name = 'cairo' version = '1.14.6' homepage = 'http://cairographics.org' @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_XZ] +glibver = '2.47.5' + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), @@ -21,9 +23,33 @@ dependencies = [ ('pixman', '0.34.0'), ('fontconfig', '2.11.94'), ('expat', '2.1.0'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), +] + +builddependencies = [ + ('renderproto', '0.11'), + ('libXext', '1.3.3'), + ('xextproto', '7.3.0'), + ('libX11', '1.6.3'), + ('xproto', '7.0.28'), + ('libxcb', '1.11.1') ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -configopts = "--enable-symbol-lookup=no" +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb new file mode 100644 index 0000000000..fb0fcbff8c --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb new file mode 100644 index 0000000000..168b2490e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb new file mode 100644 index 0000000000..be4171cde7 --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb new file mode 100644 index 0000000000..bca5ddd7ca --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb new file mode 100644 index 0000000000..7bbdcf2dc4 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000..b53c0d9a18 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb new file mode 100644 index 0000000000..12b8caece2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), + ('libX11', '1.6.3'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28') +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb new file mode 100644 index 0000000000..c7c638b6fa --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb new file mode 100644 index 0000000000..fcb767cfdb --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb new file mode 100644 index 0000000000..d818b47843 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb new file mode 100644 index 0000000000..1fe2fcb26c --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.38' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb new file mode 100644 index 0000000000..48199d0511 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb new file mode 100644 index 0000000000..9bc6335cdf --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb new file mode 100644 index 0000000000..3e787177f0 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb new file mode 100644 index 0000000000..1d32cb1ae6 --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From f73937858cb1ce3028affcc9f53f79f287f9a3af Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:21:22 +0200 Subject: [PATCH 320/722] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig libXau-1.0.8-foss-2016a.eb, add easyconfig libXdmcp-1.1.2-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 4 ++- .../l/libXau/libXau-1.0.8-foss-2016a.eb | 25 +++++++++++++++++++ .../l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 25 +++++++++++++++++++ 3 files changed, 53 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index ab395e2001..5cf49b60d8 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -25,9 +25,11 @@ dependencies = [ ('expat', '2.1.0'), ('GLib', glibver), ('libX11', '1.6.3'), + ('libXau', '1.0.8'), ('libxcb', '1.11.1'), - ('libXrender', '0.9.9'), + ('libXdmcp', '1.1.2'), ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..8694ab5ad2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c12e65e6e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 3f8d502c4b072f4e045c7ed18628e219a304cd24 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:46:56 +0200 Subject: [PATCH 321/722] modify easyconfig Blitz++-0.10-foss-2016a.eb, add easyconfig Blitz++-0.10-goolf-1.5.16.eb --- .../b/Blitz++/Blitz++-0.10-foss-2016a.eb | 9 ++------- .../b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb | 20 +++++++++++++++++++ 2 files changed, 22 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb index 03886c8db9..f91bad5dd3 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb @@ -10,16 +10,11 @@ description = """Blitz++ is a (LGPLv3+) licensed meta-template library for array toolchain = {'name': 'foss', 'version': '2016a'} sources = ['blitz-%(version)s.tar.gz'] -source_urls = ['https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', - 'download'] +source_urls = [('https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', 'download')] sanity_check_paths = { 'files': ['lib/libblitz.a'], - 'dirs': ['include/blitz/array', - 'include/blitz/gnu', - 'include/blitz/meta', - 'include/random', - 'lib/pkgconfig'], + 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb new file mode 100644 index 0000000000..f75014e6f2 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'Blitz++' +version = '0.10' + +homepage = 'http://blitz.sourceforge.net/' +description = """Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ + with a speed comparable to Fortran implementations, while preserving an object-oriented interface""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +sources = ['blitz-%(version)s.tar.gz'] +source_urls = [('https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', 'download')] + +sanity_check_paths = { + 'files': ['lib/libblitz.a'], + 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 9f9d4d40dcff4c9109de8ce909ca0e950a386531 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:53:06 +0200 Subject: [PATCH 322/722] modify easyconfig Saxon-HE-9.7.0.4-Java-1.7.0_79.eb --- .../easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb index eed56a9078..d38576ab53 100644 --- a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -2,6 +2,7 @@ easyblock = 'Tarball' name = 'Saxon-HE' version = '9.7.0.4' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://saxon.sourceforge.net' description = """Open Source SAXON XSLT processor developed by Saxonica Limited.""" @@ -9,11 +10,8 @@ description = """Open Source SAXON XSLT processor developed by Saxonica Limited. toolchain = {'name': 'dummy', 'version': ''} sources = ['SaxonHE%sJ.zip' % version.replace(".","-")] - source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s' , 'download'] -versionsuffix = '-Java-%(javaver)s' - dependencies = [('Java', '1.7.0_79')] jarfiles = ['saxon%(version_major)she.jar', 'saxon%(version_major)s-test.jar', 'saxon%(version_major)s-xqj.jar'] -- GitLab From 4c3641259118bc70d74b75893f2c24e348a1d661 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 7 Apr 2016 11:40:45 +0200 Subject: [PATCH 323/722] 1 --- .../g/GConf/GConf-3.2.6-intel-2016a.eb | 39 ++++++++++++++++ ...Python-3.0.2.0-intel-2016-Python-2.7.11.eb | 45 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb new file mode 100644 index 0000000000..118e97695c --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +homepage = 'https://projects.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('dbus-glib', '0.106'), + ('GLib', '2.47.5'), + ('GObject-Introspection', '1.47.1'), + ('libxml', '2.9.3'), + ('GTK+', '2.24.28'), +] + +configopts = '--disable-orbit ' + +sanity_check_paths = { + 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + + ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + + ['lib/libgconf-2.%s' % x for x in['a', 'so']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb new file mode 100644 index 0000000000..2bca75979e --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -0,0 +1,45 @@ +name = 'wxPython' +version = '3.0.2.0' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://www.wxpython.org' +description = """wxPython is a GUI toolkit for the Python programming language. + It allows Python programmers to create programs with a robust, + highly functional graphical user interface, simply and easily. + It is implemented as a Python extension module (native code) + that wraps the popular wxWidgets cross platform GUI library, + which is written in C++.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] + +patches = ['%(name)s_%(version)s_intel.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('expat', '2.1.0'), + ('GTK+', '2.24.28'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '0.10.36'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/wxrc'] + + ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + + ['lib/lib%s-3.0.so' % x for x in ['wx_baseu', 'wx_gtk2u_core']], + 'dirs': ['include', 'share', 'lib/python%(pyshortver)s/site-packages'] +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/wx-3.0-gtk2'], +} + +moduleclass = 'vis' -- GitLab From fb1feec5cb73661660cfa839cf2ff6aa193a2b5c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 7 Apr 2016 15:42:40 +0200 Subject: [PATCH 324/722] removed newline --- easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb index 63c3fa7e2d..6b593148b4 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb @@ -21,4 +21,4 @@ dependencies = [ ('libxml2', '2.9.3'), ] -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' -- GitLab From 7b27041bb0c383832ffb63e6f205c1f091a3934a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 15:59:16 +0200 Subject: [PATCH 325/722] add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb --- .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' -- GitLab From 690b3dbdd43db476033b8e56facd240268975327 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 16:45:13 +0200 Subject: [PATCH 326/722] add easyconfig MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb, add easyconfig libxml2-2.9.2-goolf-1.5.16.eb, add easyconfig HDF5-1.8.9-goolf-1.5.16.eb, add easyconfig Szip-2.1-goolf-1.5.16.eb --- .../h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb | 22 ++++++++++++++ .../l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb | 29 ++++++++++++++++++ ...goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 30 +++++++++++++++++++ .../s/Szip/Szip-2.1-goolf-1.5.16.eb | 23 ++++++++++++++ 4 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb new file mode 100644 index 0000000000..755c2cc7f9 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb @@ -0,0 +1,22 @@ +# Built with EasyBuild version 2.1.1 on 2015-08-05_14-22-07 +name = 'HDF5' +version = '1.8.9' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb new file mode 100644 index 0000000000..54c5dad803 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb new file mode 100644 index 0000000000..a5aa488ebe --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus' +version = '7.0.67' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a methodology + for management of complex scientific data.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['stable_release-%s.zip' % version.replace('.','-')] + +dependencies = [ + ('Java', '1.7.0_79', '', True), + ('Python', '2.7.9'), + ('HDF5', '1.8.9'), + ('libxml2', '2.9.2'), + ('zlib', '1.2.8') +] + +configopts = '--with-jdk=$JAVA_HOME' + +preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' + +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb new file mode 100644 index 0000000000..73e27f5f6c --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From ec8c9fd7d0dadd4dd1c5089f6135a0e87a76e244 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 8 Apr 2016 09:26:38 +0200 Subject: [PATCH 327/722] add easyconfig Python-2.7.9-goolf-1.5.16.eb, add easyconfig bzip2-1.0.6-goolf-1.5.16.eb, add easyconfig libreadline-6.3-goolf-1.5.16.eb, add easyconfig ncurses-5.9-goolf-1.5.16.eb, add easyconfig SQLite-3.8.8.1-goolf-1.5.16.eb, add easyconfig Tk-8.6.3-goolf-1.5.16-no-X11.eb, add easyconfig OpenSSL-1.0.1k-goolf-1.5.16.eb --- .../b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb | 15 +++ .../libreadline-6.3-goolf-1.5.16.eb | 30 +++++ .../n/ncurses/ncurses-5.9-goolf-1.5.16.eb | 36 ++++++ .../o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb | 24 ++++ .../p/Python/Python-2.7.9-goolf-1.5.16.eb | 116 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb | 38 ++++++ .../t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb | 25 ++++ 7 files changed, 284 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb new file mode 100644 index 0000000000..1f608a116f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically +compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical +compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s/'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb new file mode 100644 index 0000000000..9a2a57c200 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb new file mode 100644 index 0000000000..0d4841191f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, +and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and +function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb new file mode 100644 index 0000000000..895b5bd87b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1k' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb new file mode 100644 index 0000000000..dee7cd4fdf --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -0,0 +1,116 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), + ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb new file mode 100644 index 0000000000..6946daaee7 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb new file mode 100644 index 0000000000..b383831c92 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 2b8706a0b067912224fda3a480f910701fe0cbe4 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:19:45 +0200 Subject: [PATCH 328/722] add easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig freetype-2.6.2-foss-2016a.eb, add easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig pixman-0.34.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 29 +++++++++++++++++++ .../f/freetype/freetype-2.6.2-foss-2016a.eb | 3 +- .../p/pixman/pixman-0.34.0-foss-2016a.eb | 20 +++++++++++++ 3 files changed, 50 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb new file mode 100644 index 0000000000..4afe79dcce --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb index 41c2f0204e..3111a314be 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -14,8 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, - 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb new file mode 100644 index 0000000000..896aab1550 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 821479d0f1049f642b3f2ff7cfb9a2fca8f9206b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 10:18:48 +0200 Subject: [PATCH 329/722] 2 --- .../d/DBus/DBus-1.10.8-intel-2016a.eb | 24 +++++++++++ .../dbus-glib/dbus-glib-0.106-intel-2016a.eb | 25 +++++++++++ .../g/GConf/GConf-3.2.6-intel-2016a.eb | 5 ++- .../GST-plugins-base-0.10.36-intel-2016a.eb | 37 +++++++++++++++++ .../GStreamer-0.10.36-intel-2016a.eb | 41 +++++++++++++++++++ ...intltool-0.51.0-intel-2016a-Perl-5.22.1.eb | 25 +++++++++++ ...Python-3.0.2.0-intel-2016-Python-2.7.11.eb | 6 +++ ...XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb | 27 ++++++++++++ 8 files changed, 188 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb new file mode 100644 index 0000000000..f322881382 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.10.8' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb new file mode 100644 index 0000000000..321204b244 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.106' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GLib', '2.47.5'), + ('DBus', '1.10.8'), + ('expat', '2.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb index 118e97695c..ec87efba55 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -8,7 +8,7 @@ description = """GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.""" -toolchain = {'name': 'intel', 'version': '2014b'} +toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] @@ -17,8 +17,9 @@ dependencies = [ ('dbus-glib', '0.106'), ('GLib', '2.47.5'), ('GObject-Introspection', '1.47.1'), - ('libxml', '2.9.3'), + ('libxml2', '2.9.3'), ('GTK+', '2.24.28'), + ('intltool', '0.51.0', '-Perl-5.22.1'), ] configopts = '--disable-orbit ' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb new file mode 100644 index 0000000000..914e875639 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '0.10.36')] + +#Does not work with Bison 3 +builddependencies = [ +# ('Bison', '2.7', '', True), + ('Bison', '3.0.4'), + ('flex', '2.6.0'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-0.10' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-0.10.so' % x for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb new file mode 100644 index 0000000000..6c81f735d4 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.47.5'), + ('GObject-Introspection', '1.47.1'), + ('zlib', '1.2.8'), +] + +#Does not work with Bison 3 +builddependencies = [ +# ('Bison', '2.7', '', True), + ('Bison', '3.0.4'), + ('flex', '2.6.0'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-0.10' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-0.10.so' % x for x in ['reamer', 'base', 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..4c3bc089de --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.22.1' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.44', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb index 2bca75979e..439291d7b0 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -1,3 +1,6 @@ +easyblock = 'ConfigureMake' +#easyblock = 'PythonPackage' + name = 'wxPython' version = '3.0.2.0' versionsuffix = "-Python-%(pyver)s" @@ -31,6 +34,9 @@ dependencies = [ parallel = 1 +#options = {'modulename': 'wx'} +#skipsteps = ['install_step', 'make_installdir' ] + sanity_check_paths = { 'files': ['bin/wxrc'] + ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..5cb19baa1c --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.44' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1'), + ('expat', '2.1.0') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], +} + +moduleclass = 'data' -- GitLab From 0263a7c1eae14b20cf0d549b928a77037cdc15ce Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 10:39:37 +0200 Subject: [PATCH 330/722] Builddependencies fixed for GObject-introspection --- .../GObject-Introspection-1.42.0-intel-2014b.eb | 4 +++- .../GObject-Introspection-1.44.0-intel-2015a.eb | 3 +++ .../GObject-Introspection-1.47.1-intel-2015b.eb | 3 +++ .../GObject-Introspection-1.47.1-intel-2016a.eb | 8 +++++--- 4 files changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb index 7ae4e4f769..1f246a9bfc 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb @@ -18,9 +18,11 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.8'), ('GLib', '2.40.0'), - ('Bison', '3.0.2'), ] +builddependencies = [ + ('Bison', '3.0.2'), +] sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb index 0461a34f5f..835de46b5b 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb @@ -18,6 +18,9 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.44.1'), +] + +builddependencies = [ ('Bison', '3.0.4', '', ('GCC', '4.9.2')), ] diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb index 7bff362648..3e1f37f646 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb @@ -18,6 +18,9 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.47.1'), +] + +builddependencies = [ ('Bison', '3.0.4'), ] diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb index eaa343080d..360f641464 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -20,14 +20,16 @@ pyver = '2.7.11' dependencies = [ ('Python', pyver), ('GLib', '2.47.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), ('flex', '2.6.0'), ('Bison', '3.0.4'), ('cairo', '1.14.6'), - ('libffi', '3.2.1'), ] -builddependencies = [('Autotools', '20150215')] - preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts -- GitLab From 7b8ff1272ac3332e3a75cb50cf751cb568ae4ea2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 10:44:38 +0200 Subject: [PATCH 331/722] fixed gobject-intro builddep --- .../GObject-Introspection-1.47.1-foss-2016a.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb index 3c83530c29..2ea4584a28 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -20,14 +20,16 @@ pyver = '2.7.11' dependencies = [ ('Python', pyver), ('GLib', '2.47.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), ('flex', '2.6.0'), ('Bison', '3.0.4'), ('cairo', '1.14.6'), - ('libffi', '3.2.1'), ] -builddependencies = [('Autotools', '20150215')] - preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts -- GitLab From ab78bd9b77913e4fc297e3a80c01225d559b051b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:02:48 +0200 Subject: [PATCH 332/722] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig GLib-2.47.5-foss-2016a.eb, modify easyconfig freetype-2.6.2-foss-2016a.eb, modify easyconfig pixman-0.34.0-foss-2016a.eb, modify easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig libX11-1.6.3-foss-2016a.eb, add easyconfig libxcb-1.11.1-foss-2016a.eb, add easyconfig libXrender-0.9.9-foss-2016a.eb, add easyconfig libXext-1.3.3-foss-2016a.eb, add easyconfig renderproto-0.11-foss-2016a.eb, add easyconfig xextproto-7.3.0-foss-2016a.eb, add easyconfig xproto-7.0.28-foss-2016a.eb, add easyconfig libffi-3.2.1-foss-2016a.eb, add easyconfig gettext-0.19.7-foss-2016a.eb, add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb, add easyconfig PCRE-8.38-foss-2016a.eb, add easyconfig inputproto-2.3.1-foss-2016a.eb, add easyconfig libpthread-stubs-0.3-foss-2016a.eb, add easyconfig kbproto-1.0.7-foss-2016a.eb, add easyconfig xtrans-1.3.5-foss-2016a.eb, add easyconfig xorg-macros-1.19.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 30 +++++++++++++++-- .../g/GLib/GLib-2.47.5-foss-2016a.eb | 33 +++++++++++++++++++ .../g/gettext/gettext-0.19.7-foss-2016a.eb | 23 +++++++++++++ .../l/libXext/libXext-1.3.3-foss-2016a.eb | 1 + .../libXrender/libXrender-0.9.9-foss-2016a.eb | 4 +++ .../l/libffi/libffi-3.2.1-foss-2016a.eb | 23 +++++++++++++ .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++ .../xorg-macros-1.19.0-foss-2016a.eb | 22 +++++++++++++ 8 files changed, 164 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index 4afe79dcce..ab395e2001 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = "cairo" +name = 'cairo' version = '1.14.6' homepage = 'http://cairographics.org' @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_XZ] +glibver = '2.47.5' + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), @@ -21,9 +23,33 @@ dependencies = [ ('pixman', '0.34.0'), ('fontconfig', '2.11.94'), ('expat', '2.1.0'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), +] + +builddependencies = [ + ('renderproto', '0.11'), + ('libXext', '1.3.3'), + ('xextproto', '7.3.0'), + ('libX11', '1.6.3'), + ('xproto', '7.0.28'), + ('libxcb', '1.11.1') ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -configopts = "--enable-symbol-lookup=no" +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb new file mode 100644 index 0000000000..fb0fcbff8c --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb new file mode 100644 index 0000000000..168b2490e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index ce3e6d964e..0a0acbe42b 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -15,6 +15,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index eee347a314..12b8caece2 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -14,6 +14,10 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), + ('libX11', '1.6.3'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28') ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb new file mode 100644 index 0000000000..c7c638b6fa --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 23d49b344a3159cf6e1b84a0e873754b08789e41 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:21:22 +0200 Subject: [PATCH 333/722] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig libXau-1.0.8-foss-2016a.eb, add easyconfig libXdmcp-1.1.2-foss-2016a.eb --- easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index ab395e2001..5cf49b60d8 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -25,9 +25,11 @@ dependencies = [ ('expat', '2.1.0'), ('GLib', glibver), ('libX11', '1.6.3'), + ('libXau', '1.0.8'), ('libxcb', '1.11.1'), - ('libXrender', '0.9.9'), + ('libXdmcp', '1.1.2'), ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), ] builddependencies = [ -- GitLab From 3dcbdd98222ef584623e17fe698cf4f602897cdc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 8 Apr 2016 12:02:01 +0100 Subject: [PATCH 334/722] Update IGVTools to 2.3.72 --- .../IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb new file mode 100644 index 0000000000..af0616b491 --- /dev/null +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'IGVTools' +version = '2.3.72' + +homepage = 'http://www.broadinstitute.org/software/igv/' +description = """ This package contains command line utilities for preprocessing, + computing feature count density (coverage), sorting, and indexing data files. + See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] +sources = ['%(namelower)s_%(version)s.zip'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["igvtools.jar", "igvtools"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 4dab0a4ea3bcc8e35b8f22daab6ba0ebe764a781 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 14:42:42 +0200 Subject: [PATCH 335/722] {vis}[intel-2016a] wxPython 3.0.2.0 (REVIEW) --- .../GST-plugins-base-0.10.36-intel-2016a.eb | 4 +-- .../GStreamer-0.10.36-intel-2016a.eb | 4 +-- .../libXxf86vm-1.1.4-intel-2016a.eb | 30 +++++++++++++++++++ ...Python-3.0.2.0-intel-2016-Python-2.7.11.eb | 12 ++++---- .../w/wxPython/wxPython_3.0.2.0_intel.patch | 12 ++++++++ .../xf86vidmodeproto-2.3.1-intel-2016a.eb | 19 ++++++++++++ 6 files changed, 69 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch create mode 100644 easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index 914e875639..af962689d7 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -18,9 +18,7 @@ dependencies = [('GStreamer', '0.10.36')] #Does not work with Bison 3 builddependencies = [ -# ('Bison', '2.7', '', True), - ('Bison', '3.0.4'), - ('flex', '2.6.0'), + ('Bison', '2.7', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index 6c81f735d4..178e012daf 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -22,9 +22,7 @@ dependencies = [ #Does not work with Bison 3 builddependencies = [ -# ('Bison', '2.7', '', True), - ('Bison', '3.0.4'), - ('flex', '2.6.0'), + ('Bison', '2.7', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000..873ae3da80 --- /dev/null +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXxf86vm' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 XFree86 video mode extension library""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xf86vidmodeproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xf86vmode.h']+ + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb index 439291d7b0..4d7ba463bd 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -1,6 +1,3 @@ -easyblock = 'ConfigureMake' -#easyblock = 'PythonPackage' - name = 'wxPython' version = '3.0.2.0' versionsuffix = "-Python-%(pyver)s" @@ -30,12 +27,15 @@ dependencies = [ ('GTK+', '2.24.28'), ('GConf', '3.2.6'), ('GST-plugins-base', '0.10.36'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('libSM', '1.2.2'), + ('libXxf86vm', '1.1.4'), ] -parallel = 1 +options = {'modulename': 'wx'} -#options = {'modulename': 'wx'} -#skipsteps = ['install_step', 'make_installdir' ] +parallel = 1 sanity_check_paths = { 'files': ['bin/wxrc'] + diff --git a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch new file mode 100644 index 0000000000..ac58f0c1ac --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch @@ -0,0 +1,12 @@ +# Intel compiler have problems with precompiled headers (cannot mix C and C++ precompiled headers, like in GNU compilers) +# B. Hajgato (VUB) April 8th 2016 +--- wxPython-src-3.0.2.0/build/tools/build-wxwidgets.py.org 2014-11-27 21:49:59.000000000 +0100 ++++ wxPython-src-3.0.2.0/build/tools/build-wxwidgets.py 2016-04-08 13:03:01.362591062 +0200 +@@ -268,6 +268,7 @@ + configure_opts.append("--with-gtk=3") + + wxpy_configure_opts = [ ++ "--disable-precomp-headers", + "--with-opengl", + "--enable-sound", + "--enable-graphics_ctx", diff --git a/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb b/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb new file mode 100644 index 0000000000..3665e42444 --- /dev/null +++ b/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xf86vidmodeproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 XFree86 video mode extension protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xf86vm%s.h' % x for x in ['', 'proto', 'str']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 556b6294cd2ae5229d67cc4986caa48b4a0bcb33 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 8 Apr 2016 15:52:14 -0400 Subject: [PATCH 336/722] add ScientificPython 2.9.4 and numpy 1.10.4 for foss 2016a toolchain --- .../numpy-1.10.4-foss-2016a-Python-2.7.11.eb | 26 ++++++++++++++ ...icPython-2.9.4-foss-2016a-Python-2.7.11.eb | 35 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f2c859648a --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.10.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%(version)s-sse42.patch', +] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a597bd3eff --- /dev/null +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'ScientificPython' +version = '2.9.4' + +homepage = 'https://sourcesup.cru.fr/projects/scientific-py/' +description = """ScientificPython is a collection of Python modules for scientific computing. + It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, + and parallelization.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + # older version of numpy than the one included in Python module required + # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for + ('numpy', '1.10.4', versionsuffix), +] + +options = {'modulename': 'Scientific'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Scientific' % pyshortver], +} + +moduleclass = 'math' -- GitLab From 2f44609dc27711bf4292e2b9101d2cbac77061f1 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 8 Apr 2016 16:38:14 -0400 Subject: [PATCH 337/722] Update source_urls parameter in ScientificPython easyconfig files --- .../ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb | 2 +- .../ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb | 2 +- .../ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb index b783e38692..c1aca8b5ad 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'gmpolf', 'version': '1.4.8'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f3c253971b..65204949fb 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb index ed6a708c5f..25d50d354e 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb @@ -10,7 +10,7 @@ and parallelization.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb index 20336396df..9274b5b9ad 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb index fcc68a81ed..5aa3dd118d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'ictce', 'version': '5.2.0'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb index 997b8a1673..89a12d0943 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb index 2446abe86f..b745e7f0a4 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4411'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb index 0170615e9c..876a244102 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb index 47671f1164..857fd95a08 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] pyver = '2.7.11' -- GitLab From c74b00de25ab3199f39cde3c889c01383f1ef871 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 11:21:50 +0200 Subject: [PATCH 338/722] use XORG_LIB_SOURCE everywhere --- easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb index fa49f6c97c..78420c88a5 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb index fe3df1bbcf..289966eec9 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), -- GitLab From 1a9927879a743d52c447108463b62b095a6d15ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 12:19:03 +0200 Subject: [PATCH 339/722] add checksums in SuiteSparse easyconfigs --- .../ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb | 2 ++ .../ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb | 2 ++ .../ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb | 2 ++ 9 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb index b783e38692..ce094bf25b 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'gmpolf', 'version': '1.4.8'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f3c253971b..a89c80a516 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb index ed6a708c5f..51bacf787c 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb index 20336396df..a889a4de4d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb index fcc68a81ed..2c70b32004 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '5.2.0'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb index 997b8a1673..e0938abda4 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb index 2446abe86f..feb8f56c9d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2014b'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['73ee0df19c7b58cdf2954261f0763c77'] + python = "Python" pythonversion = '2.7.8' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb index 0170615e9c..01aca5b107 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] sources = [SOURCE_TAR_GZ] +checksums = ['dc2987089e106cb807b4ccecf7adc071'] + python = 'Python' pythonversion = '2.7.9' pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb index 47671f1164..20da6ee305 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] sources = [SOURCE_TAR_GZ] +checksums = ['dc2987089e106cb807b4ccecf7adc071'] + pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[:2]) -- GitLab From ff6955fedb6d0c154f4ab0b3d8f057f986c215d7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 9 Apr 2016 12:10:39 +0100 Subject: [PATCH 340/722] Initial version of bam-readcount --- ...readcount-0.7.4-cmake_install_prefix.patch | 12 +++++++ .../bam-readcount-0.7.4-foss-2015b.eb | 35 +++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch create mode 100644 easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch new file mode 100644 index 0000000000..2916d1f5e7 --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch @@ -0,0 +1,12 @@ +diff -u bam-readcount-0.7.4/CMakeLists.txt bam-readcount-0.7.4.new/CMakeLists.txt +--- bam-readcount-0.7.4/CMakeLists.txt 2014-12-07 19:45:03.000000000 +0000 ++++ bam-readcount-0.7.4.new/CMakeLists.txt 2016-04-06 22:06:12.336807391 +0100 +@@ -2,7 +2,7 @@ + + project(bam-readcount) + +-set(CMAKE_INSTALL_PREFIX "/usr") ++#set(CMAKE_INSTALL_PREFIX "/usr") + set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake;${CMAKE_SOURCE_DIR}/build-common/cmake") + include(TestHelper) + include(VersionHelper) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb new file mode 100644 index 0000000000..b19ba9482c --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'CMakeMake' + +name = 'bam-readcount' +version = '0.7.4' + +homepage = 'https://github.com/genome/bam-readcount' +description = """Count DNA sequence reads in BAM files""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/genome/%(name)s/archive'] + +patches = ['%(name)s-%(version)s-cmake_install_prefix.patch'] + +builddependencies = [ + ('SAMtools', '1.3'), + ('CMake', '3.4.1'), +] + +configopts = " -DCMAKE_INSTALL_PREFIX=%(installdir)s " + +prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&" + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/bam-readcount"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 09e71b456c69f7db1a62915a145b1dab23b5e952 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 15:21:46 +0200 Subject: [PATCH 341/722] use XORG_PROTO_SOURCE + 'env' in preconfigopts --- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb index 0d7fd4a4a2..1fbffb2758 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb index d26077ac1e..850097aee1 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb index 75924f159f..c39482e40c 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index c9dd66c1c1..fb2151e5df 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, -- GitLab From 68db97d838656d94d12133f292533dc2670c42f0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 9 Apr 2016 14:51:56 +0100 Subject: [PATCH 342/722] Remove obsolete configopts and add explanation/authorship to patch --- .../bam-readcount-0.7.4-cmake_install_prefix.patch | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch index 2916d1f5e7..aecba22db8 100644 --- a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch @@ -1,3 +1,7 @@ +# patch to remove hard-coded installation prefix +# Adam Huffman +# The Francis Crick Institute + diff -u bam-readcount-0.7.4/CMakeLists.txt bam-readcount-0.7.4.new/CMakeLists.txt --- bam-readcount-0.7.4/CMakeLists.txt 2014-12-07 19:45:03.000000000 +0000 +++ bam-readcount-0.7.4.new/CMakeLists.txt 2016-04-06 22:06:12.336807391 +0100 -- GitLab From 86e08e86be0bf0b7717a15b4bd15b9ace3b60c60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 16:37:07 +0200 Subject: [PATCH 343/722] sync preconfigopts/buildopts in GObject-Introspection 1.47.1 easyconfigs --- .../GObject-Introspection-1.47.1-intel-2015b.eb | 5 +++++ .../GObject-Introspection-1.47.1-intel-2016a.eb | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb index 3e1f37f646..42f9c4f97f 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb @@ -24,6 +24,11 @@ builddependencies = [ ('Bison', '3.0.4'), ] +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb index 360f641464..7606731e75 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -30,7 +30,7 @@ builddependencies = [ ('cairo', '1.14.6'), ] -preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -- GitLab From ebb1e4c1d3f91f420161ddacb12c4270b9380e84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 16:39:35 +0200 Subject: [PATCH 344/722] sync (build) deps in GObject-Introspection 1.47.1 easyconfigs --- .../GObject-Introspection-1.47.1-intel-2015b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb index 42f9c4f97f..b1d634cd35 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb @@ -18,10 +18,14 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.47.1'), + ('libffi', '3.2.1'), ] builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), ('Bison', '3.0.4'), + ('cairo', '1.14.4'), ] preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " -- GitLab From d0eedfe69ed10024cd995cb170fddb0d1467732d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 17:27:10 +0200 Subject: [PATCH 345/722] various small style fixes --- .../GObject-Introspection-1.47.1-foss-2016a.eb | 6 ++---- easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb | 1 + .../l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb | 1 + easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb | 1 + easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb | 1 + easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb | 1 + .../m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb | 2 +- .../m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb | 2 +- .../m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb | 2 +- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 2 +- .../m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb | 2 +- .../m/makedepend/makedepend-1.0.5-intel-2015a.eb | 2 +- .../m/makedepend/makedepend-1.0.5-intel-2015b.eb | 2 +- .../m/makedepend/makedepend-1.0.5-intel-2016a.eb | 2 +- 19 files changed, 20 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb index 2ea4584a28..ef2d0a1446 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -15,10 +15,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -pyver = '2.7.11' - dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ('GLib', '2.47.5'), ('libffi', '3.2.1'), ] @@ -30,7 +28,7 @@ builddependencies = [ ('cairo', '1.14.6'), ] -preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb index 6943d3e084..68589245d1 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb index eaa232fe89..cd973d2ea0 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' versionsuffix = '-Python-2.7.11' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb index 0ed8e42a20..60cd626d31 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb index bd92d68db6..c94df236e0 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.6' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb index 265985f5e5..5e9d4cb87a 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.6' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb index 3b30e0e1d5..6fb02db3e5 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb index 393090c994..00c6dd2232 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb index f5f634beae..82ed5ca658 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] patches = ['makedepend_icc-sigaction.patch'] diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb index 25ba8c0849..c4b315a1b7 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb index 858f7c2608..255cd2ad52 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb index 808282ac91..49f692fd43 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb index 873b6391a2..ece06f94eb 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb index 07b6b524bf..50e1707937 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] patches = ['makedepend_icc-sigaction.patch'] diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index 8bd95eee91..863911703e 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb index c92d8634e2..38d76d37d2 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb index 0b36b37c50..282179280a 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb index 77541afc67..ca6025105b 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb index 1158bd68be..e38d07d26e 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], -- GitLab From 25115093469d2add35217998147dd08a68ce16aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 18:34:13 +0200 Subject: [PATCH 346/722] use XORG_PROTO_SOURCE --- .../x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb index a40280e419..fdbb9a1f7d 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], -- GitLab From 6e3de4adfa74be7ef5b164931fa37c5dba22be68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 20:23:28 +0200 Subject: [PATCH 347/722] clean up wxPython easyconfig according to enhancements to wxPython easyblock --- .../wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb index 4d7ba463bd..803388b88a 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -33,19 +33,4 @@ dependencies = [ ('libXxf86vm', '1.1.4'), ] -options = {'modulename': 'wx'} - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/wxrc'] + - ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + - ['lib/lib%s-3.0.so' % x for x in ['wx_baseu', 'wx_gtk2u_core']], - 'dirs': ['include', 'share', 'lib/python%(pyshortver)s/site-packages'] -} - -modextrapaths = { - 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/wx-3.0-gtk2'], -} - moduleclass = 'vis' -- GitLab From 71405555deacf3b3a4280055e2b11d53317629f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 20:35:55 +0200 Subject: [PATCH 348/722] style fixes --- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb | 1 - .../GST-plugins-base-0.10.36-intel-2016a.eb | 6 +++--- .../g/GStreamer/GStreamer-0.10.36-intel-2016a.eb | 9 +++++---- .../intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb index ec87efba55..89fe1cefe2 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -37,4 +37,3 @@ modextrapaths = { } moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index af962689d7..f2d1e756a5 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -16,14 +16,14 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [('GStreamer', '0.10.36')] -#Does not work with Bison 3 +# does not work with Bison 3.x builddependencies = [ ('Bison', '2.7', '', True), ] sanity_check_paths = { - 'files': ['bin/gst-%s-0.10' % x for x in ['discoverer', 'visualise']] + - ['lib/libgst%s-0.10.so' % x for x in ['app', 'audio', 'video']], + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index 178e012daf..ccd3a73617 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -20,15 +20,16 @@ dependencies = [ ('zlib', '1.2.8'), ] -#Does not work with Bison 3 +# does not work with Bison 3.x builddependencies = [ ('Bison', '2.7', '', True), ] sanity_check_paths = { - 'files': ['bin/gst-%s-0.10' % x for x in ['inspect', 'typefind', 'launch']] + - ['lib/libgst%s-0.10.so' % x for x in ['reamer', 'base', 'controller', 'check']], - 'dirs': ['include', 'share', 'libexec'] + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['reamer', 'base', + 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'], } modextrapaths = { diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb index 4c3bc089de..0b9db08cff 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb @@ -10,7 +10,7 @@ description = """intltool is a set of tools to centralize translation of toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] dependencies = [ -- GitLab From 9fe4ba351aca7af665bb92fb5ce3a5220bb630a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Apr 2016 10:47:20 +0200 Subject: [PATCH 349/722] fix typo in filename for wxPython --- ...on-2.7.11.eb => wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/w/wxPython/{wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb => wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb rename to easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb -- GitLab From 8ac5aefb82cd2237cd679ba3c103e973ee3f9581 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 10 Apr 2016 16:00:31 +0200 Subject: [PATCH 350/722] Fix build/runtime dependencies --- .../easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index 12b8caece2..1e63340752 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -14,7 +14,6 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), - ('libX11', '1.6.3'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28') -- GitLab From 75e2d85779aa974e7c506e0a95547fa6618ddc73 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 10 Apr 2016 21:26:14 +0100 Subject: [PATCH 351/722] Really remove the obsolete configopts this time --- .../b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb index b19ba9482c..a786a5b208 100644 --- a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -21,8 +21,6 @@ builddependencies = [ ('CMake', '3.4.1'), ] -configopts = " -DCMAKE_INSTALL_PREFIX=%(installdir)s " - prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&" separate_build_dir = True -- GitLab From e3800389846428f835f7674d1e3a9d31923189c2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 10 Apr 2016 23:17:21 +0100 Subject: [PATCH 352/722] Port GROMACS 5.1.2 to foss-2016a --- .../GROMACS-5.1.2-foss-2016a-hybrid.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb new file mode 100644 index 0000000000..5b189abdbd --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +# +# Version 5.1.2 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.2' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.4.1'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.60.0')] + +moduleclass = 'bio' -- GitLab From 0382afb4bd7cb2f5c50dd5364d7090eb238747df Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 10 Apr 2016 23:50:25 +0100 Subject: [PATCH 353/722] Update libxml2 to 2.9.3 for foss-2016a --- .../easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb index 5b189abdbd..e699b7dd9b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb @@ -31,7 +31,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.4.1'), - ('libxml2', '2.9.2') + ('libxml2', '2.9.3') ] dependencies = [('Boost', '1.60.0')] -- GitLab From 22adb35c727a98b0064b959c40b49d646e055e9b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 11 Apr 2016 09:27:41 +0100 Subject: [PATCH 354/722] Add missing zlib dep and change samtools to normal, not build dep --- .../b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb index a786a5b208..9f5b2f295c 100644 --- a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -17,10 +17,14 @@ source_urls = ['https://github.com/genome/%(name)s/archive'] patches = ['%(name)s-%(version)s-cmake_install_prefix.patch'] builddependencies = [ - ('SAMtools', '1.3'), ('CMake', '3.4.1'), ] +dependencies = [ + ('SAMtools', '1.3'), + ('zlib', '1.2.8'), +] + prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&" separate_build_dir = True -- GitLab From a7b47e4ad40b160fb4989ad4cf48697e6006e266 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 10:34:28 +0200 Subject: [PATCH 355/722] foss 2016a version for sparsehash --- .../sparsehash/sparsehash-2.0.2-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb new file mode 100644 index 0000000000..062c5abe5e --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.2' + +homepage = 'https://code.google.com/p/sparsehash/' +description = """An extremely memory-efficient hash_map + implementation. 2 bits/entry overhead! The SparseHash library + contains several hash-map implementations, including + implementations that optimize for space or speed.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sparsehash.googlecode.com/files/'] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' \ No newline at end of file -- GitLab From 52b1c35a20d08cd618263ffe10d9108548360361 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 10:37:50 +0200 Subject: [PATCH 356/722] removed newline --- .../easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb index 062c5abe5e..d835154d86 100644 --- a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb @@ -20,4 +20,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'devel' \ No newline at end of file +moduleclass = 'devel' -- GitLab From 8cf5d34294607fb7c056c4c581f26444a3152e68 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 10:45:57 +0200 Subject: [PATCH 357/722] foss 2016a version for ABySS --- .../a/ABySS/ABySS-1.9.0-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb new file mode 100644 index 0000000000..1aff3781e1 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Maxime Schmitt , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.9.0' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] + +dependencies = [('Boost', '1.60.0')] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From f7ac943a2ff6f9d2719bd0ca4d704cbf3af38622 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Apr 2016 11:52:51 +0200 Subject: [PATCH 358/722] add easyconfig pandas-0.18.0-intel-2016a-Python-2.7.11.eb, add easyconfig pandas-0.18.0-intel-2016a-Python-3.5.1.eb --- ...pandas-0.18.0-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ .../pandas-0.18.0-intel-2016a-Python-3.5.1.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..69e84f6fa3 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..a3d2dbb5d1 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 446c86fc8446d9ceff2641644de5b40c79318f99 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 12:33:47 +0200 Subject: [PATCH 359/722] Dependency of sparsehash --- easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb index 1aff3781e1..46ae6d041a 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -22,7 +22,10 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] -dependencies = [('Boost', '1.60.0')] +dependencies = [ + ('Boost', '1.60.0'), + (sparsehash, '2.0.2') +] sanity_check_paths = { 'files': ["bin/ABYSS", "bin/ABYSS-P"], -- GitLab From 807626f4d5d2ea884882a3fd8da582245e8726ee Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 14:44:56 +0200 Subject: [PATCH 360/722] add easyconfig Tcl-8.6.3-goolf-1.5.16.eb --- .../t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb new file mode 100644 index 0000000000..a8f55caa25 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From 100f5c6abb616bfeb897c14a99b9023787f0ff6f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 14:52:11 +0200 Subject: [PATCH 361/722] Remove comment from HDF5-1.8.9-goolf-1.5.16.eb --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb index 755c2cc7f9..46dd3d15ad 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.1 on 2015-08-05_14-22-07 name = 'HDF5' version = '1.8.9' -- GitLab From c65cce06d6b0a92d173c96e87a6161f06a4b0a74 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 14:53:58 +0200 Subject: [PATCH 362/722] Comment out OpenSSL dependency in Python-2.7.9-goolf-1.5.16.eb --- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index dee7cd4fdf..d726f06367 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -21,7 +21,7 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), - ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -- GitLab From 2d01f15bc0ff258e333b4110d1e60ba413e6dbb3 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:03:51 +0200 Subject: [PATCH 363/722] Use https where possible in Python-2.7.9-goolf-1.5.16.eb --- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index d726f06367..70860e49fa 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -40,16 +40,16 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'source_urls': [('https://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], }), ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + 'source_urls': [('https://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], -- GitLab From 8acce97e99dd80a6fdad06c62cdc1f01b396b3fc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:04:46 +0200 Subject: [PATCH 364/722] Correct preconfigopts in libreadline-6.3-goolf-1.5.16.eb --- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb index 9a2a57c200..a11e7823ed 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + -- GitLab From 3752406eadac2b7d4b7f5b2f98a206b441b0d5de Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:14:10 +0200 Subject: [PATCH 365/722] Restrict parallel build in MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index a11de24d4f..5af25d6b8e 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -23,6 +23,6 @@ configopts = '--with-jdk=$JAVA_HOME' preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' -buildopts = '-j 1' +parallel = 1 moduleclass = 'data' -- GitLab From 179a5fc322d8db28072e25ddf7c30851a389f14e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:18:20 +0200 Subject: [PATCH 366/722] Wrap description to <120 characters in MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 5af25d6b8e..6a1d121ef8 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -5,7 +5,8 @@ version = '7.0.67' versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' homepage = 'http://mdsplus.org/' -description = """MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.""" +description = """MDSplus is a set of software tools for data acquisition and storage and a + methodology for management of complex scientific data.""" toolchain = {'name': 'foss', 'version': '2016a'} -- GitLab From 472992ac0f7f131dcd519fa2fed53114f1a27e0f Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 11 Apr 2016 16:01:43 +0200 Subject: [PATCH 367/722] Beast latest version using foss-2016a --- .../b/Beast/Beast-2.4.0-foss-2016a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb new file mode 100644 index 0000000000..68cf147acc --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'Beast' +version = '2.4.0' + +homepage = 'http://beast2.org/' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%(version)s.Linux.tgz'] + + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '2_1_2', '', ('foss', '2016a')), +] + +sanity_check_paths = { + 'files': ["bin/beast"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From a6397ef10bccd4aa65c1bc309b57c3a3cc40321d Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 11 Apr 2016 16:06:53 +0200 Subject: [PATCH 368/722] latest beagle-lib support foss2016a --- .../beagle-lib/beagle-lib-2_1_2-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb new file mode 100644 index 0000000000..033afea4f8 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '2_1_2' + +homepage = 'http://code.google.com/p/beagle-lib/' +description = """ +beagle-lib is a high-performance library that can perform the core +calculations at the heart of most Bayesian and Maximum Likelihood +phylogenetics packages. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['beagle_release_%(version)s.tar.gz'] + +dependencies = [('Java', '1.7.0_15', '', True)] + +# parallel build does not work (to test) +parallel = 1 + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From edeed474f2fd36ab442256811a34bc917853649b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 17:27:04 +0200 Subject: [PATCH 369/722] quickfix quotes for sparsehash dependency --- easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb index 46ae6d041a..442c127432 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -24,7 +24,7 @@ source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] dependencies = [ ('Boost', '1.60.0'), - (sparsehash, '2.0.2') + ('sparsehash', '2.0.2') ] sanity_check_paths = { -- GitLab From e2ca621fcc6de9d3d7acd6a59c8f150370f1c588 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 14:48:56 -0400 Subject: [PATCH 370/722] using numpy 1.8.2 that support oldnumeric and makes compatible with Scientificpython --- ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 44 +++++++++++++++++++ ...icPython-2.9.4-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..182905c4bb --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index a597bd3eff..ef29eaf445 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ ('Python', pyver), # older version of numpy than the one included in Python module required # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for - ('numpy', '1.10.4', versionsuffix), + ('numpy', '1.8.2', versionsuffix), ] options = {'modulename': 'Scientific'} -- GitLab From a947b9c9d89fc88a92ac4a55183a037922b70dad Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 15:04:46 -0400 Subject: [PATCH 371/722] add easyconfig numpy 1.8.2 for foss --- ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 44 ------------------- ...> numpy-1.8.2-foss-2016a-Python-2.7.11.eb} | 14 +++--- 2 files changed, 7 insertions(+), 51 deletions(-) delete mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb rename easybuild/easyconfigs/n/numpy/{numpy-1.10.4-foss-2016a-Python-2.7.11.eb => numpy-1.8.2-foss-2016a-Python-2.7.11.eb} (82%) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index 182905c4bb..0000000000 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'Bundle' - -name = 'matplotlib' -version = '1.5.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - -dependencies = [ - ('Python', '2.7.11'), - ('freetype', '2.6.2'), - ('libpng', '1.6.21'), -] - -exts_list = [ - ('Cycler', '0.9.0', { - 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], - 'source_tmpl': 'cycler-%(version)s.tar.gz', - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), -] - -# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module -full_sanity_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb similarity index 82% rename from easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb index f2c859648a..e591de8fe1 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb @@ -1,6 +1,5 @@ name = 'numpy' -version = '1.10.4' -versionsuffix = '-Python-%(pyver)s' +version = '1.8.2' homepage = 'http://www.numpy.org' description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: @@ -14,13 +13,14 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = [ - 'numpy-1.8.0-mkl.patch', - 'numpy-%(version)s-sse42.patch', -] +patches = ['numpy-1.8.1-mkl.patch'] + +python = 'Python' +pyver = '2.7.11' +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('Python', '2.7.11'), + (python, pyver), ] moduleclass = 'math' -- GitLab From af9773821329739f983ee9983353627e0b1d673c Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 16:06:16 -0400 Subject: [PATCH 372/722] matplotlib 1.5.1 for foss 2016a --- ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..182905c4bb --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From d297900bdcad241d8e042b2c8136cd5f3044995b Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 17:42:22 -0400 Subject: [PATCH 373/722] add easyconfig files for git 2.8.0 foss toolchain --- .../g/gettext/gettext-0.19.7-foss-2016a.eb | 23 +++++++++++++ .../easyconfigs/g/git/git-2.8.0-foss-2016a.eb | 33 +++++++++++++++++++ .../p/Perl/Perl-5.22.1-foss-2016a-bare.eb | 17 ++++++++++ 3 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb new file mode 100644 index 0000000000..168b2490e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb b/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb new file mode 100644 index 0000000000..37fb210f88 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.8.0' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +dependencies = [ + ('cURL', '7.47.0'), + ('expat', '2.1.0'), + ('gettext', '0.19.7'), + ('Perl', '5.22.1', '-bare'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb new file mode 100644 index 0000000000..9234ed61fa --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.22.1' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' -- GitLab From c35baf4c311b0abecf3fb9e6942386f6bca79b0e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:35:06 +0200 Subject: [PATCH 374/722] correctly specify Perl location in git easyconfig --- easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index 6a03e95dba..d8dcaa74d8 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -36,7 +36,7 @@ preconfigopts = 'make configure && ' # Work around git build system bug. If LIBS contains -lpthread, then configure # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--with-perl=${EBPERLROOT} --enable-pthreads='-lpthread'" +configopts = "--with-perl=${EBPERLROOT}/bin/perl --enable-pthreads='-lpthread'" sanity_check_paths = { 'files': ['bin/git'], -- GitLab From 3ab69db466b5c4491146598c3e23f17c9fc52191 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:39:03 +0200 Subject: [PATCH 375/722] add easyconfig MultiNest-3.10-intel-2016a.eb --- .../m/MultiNest/MultiNest-3.10-intel-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb b/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb new file mode 100644 index 0000000000..78d3266bf6 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'MultiNest' +version = '3.10' + +homepage = 'https://ccpforge.cse.rl.ac.uk/gf/project/multinest/' +description = """MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space + which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# download via https://ccpforge.cse.rl.ac.uk/gf/project/multinest/frs (requires registration) +sources = ['MultiNest_v%(version)s_CMake.tar.gz'] +checksums = ['a4ed7c15f2fbbf7f859f565734fc5296'] + +builddependencies = [('CMake', '3.4.3')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ackley', 'eggboxC', 'eggboxC++', 'gaussian', 'gauss_shell', 'himmelblau', + 'obj_detect', 'rosenbrock']] + + ['lib/lib%s' % x for x in ['multinest.a', 'multinest_mpi.a', 'multinest_mpi.%s' % SHLIB_EXT, + 'multinest.%s' % SHLIB_EXT]] + + ['include/multinest.h'], + 'dirs': ['modules'], +} + +moduleclass = 'tools' -- GitLab From 04e53f7a24ab360a3f3812526116aafc8a73a421 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:39:58 +0200 Subject: [PATCH 376/722] fix typo --- easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index d8dcaa74d8..1da07f9d58 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -36,7 +36,7 @@ preconfigopts = 'make configure && ' # Work around git build system bug. If LIBS contains -lpthread, then configure # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--with-perl=${EBPERLROOT}/bin/perl --enable-pthreads='-lpthread'" +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" sanity_check_paths = { 'files': ['bin/git'], -- GitLab From fbb3f0cd75ab28fb77e3c558f35ab2a8c6117da8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:42:31 +0200 Subject: [PATCH 377/722] add easyconfig CMake-3.5.1-intel-2016a.eb --- .../c/CMake/CMake-3.5.1-intel-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb new file mode 100644 index 0000000000..a70441375c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From d2dbcc47e9b38f23d53272986bfbc28aa15faaaf Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 12 Apr 2016 11:32:03 +0200 Subject: [PATCH 378/722] fix beagle-lib dependency --- easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb index 68cf147acc..484da63909 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb @@ -21,12 +21,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] sources = ['BEAST.v%(version)s.Linux.tgz'] - dependencies = [ # this is not mandatory but beagle-lib is recommended by developers # beagle-lib will also load the required java dependency # if you remove this you should add the java dependency - ('beagle-lib', '2_1_2', '', ('foss', '2016a')), + ('beagle-lib', '2.1.2'), ] sanity_check_paths = { -- GitLab From 2b7c6d3f7ccd97633b3f77e36d3083ecc8135c8f Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 12 Apr 2016 11:34:32 +0200 Subject: [PATCH 379/722] fix java version, naming, builddependencies --- .../beagle-lib/beagle-lib-2.1.2-foss-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb new file mode 100644 index 0000000000..29785ed5e6 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '2.1.2' +homepage= 'https://github.com/beagle-dev/beagle-lib' +description = """ +beagle-lib is a high-performance library that can perform the core +calculations at the heart of most Bayesian and Maximum Likelihood +phylogenetics packages. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] + +dependencies = [('Java', '1.8.0_74', '', True)] + +builddependencies = [('Autotools', '20150215')] + +# parallel build does not work (to test) +parallel = 1 + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 18e01e189a43b9ad3c3f6c356919cb8808dd7f39 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 12 Apr 2016 13:25:43 +0200 Subject: [PATCH 380/722] removed bad beagle-lib --- .../beagle-lib/beagle-lib-2_1_2-foss-2016a.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb deleted file mode 100644 index 033afea4f8..0000000000 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'beagle-lib' -version = '2_1_2' - -homepage = 'http://code.google.com/p/beagle-lib/' -description = """ -beagle-lib is a high-performance library that can perform the core -calculations at the heart of most Bayesian and Maximum Likelihood -phylogenetics packages. -""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz -source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] -sources = ['beagle_release_%(version)s.tar.gz'] - -dependencies = [('Java', '1.7.0_15', '', True)] - -# parallel build does not work (to test) -parallel = 1 - -preconfigopts = "./autogen.sh && " - -sanity_check_paths = { - 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile - for includefile in ["beagle.h", "platform.h"]] + - ["lib/libhmsbeagle%s.so" % libfile - for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], - 'dirs': [] -} - -moduleclass = 'numlib' -- GitLab From 4a944ea2fd093c34ea0941a39499c694fd26d6b0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 14:32:26 +0200 Subject: [PATCH 381/722] dependency for SQLite --- easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb index 442c127432..aa09a6e789 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -23,8 +23,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] dependencies = [ - ('Boost', '1.60.0'), - ('sparsehash', '2.0.2') + ('Boost', '1.60.0'), + ('sparsehash', '2.0.2'), + ('SQLite', '3.9.2'), ] sanity_check_paths = { -- GitLab From 7724b2dfaa1a7cfb474d0c1c7b188dd796ce53b3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 15:42:21 +0200 Subject: [PATCH 382/722] ANTLR with foss 2016a --- .../ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a69233b272 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = "2.7.7" + +homepage = 'http://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_includes.patch'] + +pythonversion = '2.7.11' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ + ('Java', '1.8.0_74', '', True), + ('Python', pythonversion), +] + +configopts = '--disable-examples --disable-csharp ' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' -- GitLab From 2b1307343774ae1202878dfafa731a4a6d2f09d0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 16:46:02 +0200 Subject: [PATCH 383/722] BayesAss with foss 2016a --- .../b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb new file mode 100644 index 0000000000..3e78699b7f --- /dev/null +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'BayesAss' +version = '3.0.3' + +homepage = 'http://www.rannala.org/?page_id=245' description = """ +BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +sources = ['BA3-%(version)s.tar.gz'] +source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%s/src/' % +version] +dependencies = [ + ('GSL','1.16') +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["BA3"]], + 'dirs' : ['bin','include'] +} + +moduleclass = 'bio' -- GitLab From 4a1fe16ac37a29bdf91da0c140fc6b92f3e7809d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 16:54:33 +0200 Subject: [PATCH 384/722] newline added --- easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 3e78699b7f..9f74a15dd0 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -3,7 +3,8 @@ easyblock = 'ConfigureMake' name = 'BayesAss' version = '3.0.3' -homepage = 'http://www.rannala.org/?page_id=245' description = """ +homepage = 'http://www.rannala.org/?page_id=245' +description = """ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes """ -- GitLab From 441d862ecefdf2adc6222a07a7b2129f618ec502 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:09:00 +0200 Subject: [PATCH 385/722] HTSlib for foss 2016a --- .../h/HTSlib/HTSlib-1.3-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb new file mode 100644 index 0000000000..7f85666c7d --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.3' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' \ No newline at end of file -- GitLab From 6e446908e5bb57328bccdb45bc08d8e751ec8fa9 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:11:17 +0200 Subject: [PATCH 386/722] removed newline --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb index 7f85666c7d..93d7d3c6df 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb @@ -24,4 +24,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From bd6af2e81b9f53060da3ebb1a51fc7abdd4f69ae Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:13:57 +0200 Subject: [PATCH 387/722] BCFtools for foss 2016a --- .../b/BCFtools/BCFtools-1.3-foss-2016a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb new file mode 100644 index 0000000000..fe8eabe029 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.3' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [ + ('HTSlib', '1.3'), + ('zlib', '1.2.8'), + ('GSL', '1.16'), +] + +parallel = 1 + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/plugins', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['lib/plugins'], +} + +moduleclass = 'bio' -- GitLab From 0330bcc156ccb9096c94cdee4b1c7c9c479577db Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:23:53 +0200 Subject: [PATCH 388/722] quickfix version number --- .../easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 9f74a15dd0..b10287dfdd 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -1,14 +1,14 @@ easyblock = 'ConfigureMake' name = 'BayesAss' -version = '3.0.3' +version = '3.0.4' homepage = 'http://www.rannala.org/?page_id=245' description = """ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes """ -toolchain = {'name': 'foss', 'version': '2016a'} +toolchain = {'name': 'foss','version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%s/src/' % version] @@ -19,7 +19,7 @@ dependencies = [ runtest = 'check' sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["BA3"]], + 'files': [bin/BA3], 'dirs' : ['bin','include'] } -- GitLab From e4b84a2bc7e5e6f95e21523fb6b05320e33780a9 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 12 Apr 2016 15:29:39 -0500 Subject: [PATCH 389/722] Changing the version (Date Format) and also adding instructions to rename the downloaded file to lx-%(version)s.zip --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 69196eb784..9830a06815 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -5,7 +5,7 @@ easyblock = "PackedBinary" name = 'MRIcron' -version = '06_22_15' +version = '20150601' homepage = 'http://www.mccauslandcenter.sc.edu/mricro/mricron/' description = """ MRIcron allows viewing of medical images. It @@ -17,8 +17,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Automatic Download doesn't work for this software as you need to accept their license, # so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ -# and place it in a folder where Easybuild can see it. -sources = ['lx.zip'] +# and place it in a folder where Easybuild can see it. +# Also rename the zip file to lx-20150601.zip +sources = ['lx-%(version)s.zip'] checksums = ['a2d8b1c053384220953f6b670d0fd4df'] -- GitLab From d25771501a9f87623f013f7f34c643b824846f50 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 12 Apr 2016 15:51:36 -0500 Subject: [PATCH 390/722] Renaming the Easyconfig from easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb -> easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb --- .../m/MRIcron/{MRIcron-06_22_15.eb => MRIcron-20150601.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MRIcron/{MRIcron-06_22_15.eb => MRIcron-20150601.eb} (100%) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb similarity index 100% rename from easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb rename to easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb -- GitLab From 428e635f7c6c76b6e89bba45dc64e263930df681 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 12 Apr 2016 23:01:13 +0200 Subject: [PATCH 391/722] Add missing zlib dependency to MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 6a1d121ef8..b1dbee0965 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -17,7 +17,8 @@ dependencies = [ ('Java', '1.7.0_79', '', True), ('Python', '2.7.11'), ('HDF5', '1.8.16'), - ('libxml2', '2.9.3', '-Python-%(pyver)s') + ('libxml2', '2.9.3', '-Python-%(pyver)s'), + ('zlib', '1.2.8') ] configopts = '--with-jdk=$JAVA_HOME' -- GitLab From 2a277f236dbba0ad4e31f680f65d5ac4f5d4da27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Apr 2016 07:35:25 +0200 Subject: [PATCH 392/722] fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender --- easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb | 4 ++++ easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 1 + .../easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb | 3 +++ 3 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb index 2966a85fa7..a289e5fb02 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb @@ -28,9 +28,13 @@ dependencies = [ ('libxcb', '1.11.1'), ('libXrender', '0.9.9'), ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), ] builddependencies = [ ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 2b4eff3bde..2d93058e5e 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -15,6 +15,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index eee347a314..1e63340752 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -14,6 +14,9 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28') ] dependencies = [ -- GitLab From b9067f93645bb3e7ac817334393b612f4d21ad47 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 10:50:26 +0200 Subject: [PATCH 393/722] fix (pyver)s --- .../a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb index a69233b272..ddbfe7c092 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'ANTLR' version = "2.7.7" +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.antlr2.org/' description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) @@ -16,12 +17,9 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] -pythonversion = '2.7.11' -versionsuffix = "-Python-%s" % pythonversion - dependencies = [ ('Java', '1.8.0_74', '', True), - ('Python', pythonversion), + ('Python', '2.7.11'), ] configopts = '--disable-examples --disable-csharp ' -- GitLab From 46471130a735bf0c4bcc673d57e4f92dc0128e01 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 13 Apr 2016 10:19:44 +0100 Subject: [PATCH 394/722] Update rtracklayer to 1.30.4 --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 2 +- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 78a36e128c..60ddc2ec31 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -80,7 +80,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.3', bioconductor_options), + ('rtracklayer', '1.30.4', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index 42093e636a..75d2568589 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -79,7 +79,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.3', bioconductor_options), + ('rtracklayer', '1.30.4', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), -- GitLab From b38448a86b6ed9d38ab6d5653d2582a50ddbae0d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:39:21 +0200 Subject: [PATCH 395/722] quickfixes, but still needs GSL-2.1 dependency --- .../easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index b10287dfdd..ba5608e32b 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -10,8 +10,9 @@ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes toolchain = {'name': 'foss','version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] -source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%s/src/' % -version] + +source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/'] + dependencies = [ ('GSL','1.16') ] @@ -20,7 +21,7 @@ runtest = 'check' sanity_check_paths = { 'files': [bin/BA3], - 'dirs' : ['bin','include'] + 'dirs' : ['bin', 'include'] } moduleclass = 'bio' -- GitLab From 49bf25ee263585f62beec59942007be8f3dbce47 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:39:49 +0200 Subject: [PATCH 396/722] GSL-2.1 dependency --- easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index ba5608e32b..97b9dbe142 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -14,7 +14,7 @@ sources = ['BA3-%(version)s.tar.gz'] source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/'] dependencies = [ - ('GSL','1.16') + ('GSL','2.1') ] runtest = 'check' -- GitLab From 2de7a18c82c6442ebb2bc246fbb2964a4c4ce511 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:42:36 +0200 Subject: [PATCH 397/722] GSL for foss 2016a --- .../easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb new file mode 100644 index 0000000000..f4a28c0d8f --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = "2.1" + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'version': '2016a', 'name': 'foss'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' -- GitLab From db2effc74e8f575a3632e68206455bab132a3fcd Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:49:49 +0200 Subject: [PATCH 398/722] missing quotes --- easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 97b9dbe142..0dc4a540af 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -20,7 +20,7 @@ dependencies = [ runtest = 'check' sanity_check_paths = { - 'files': [bin/BA3], + 'files': ['bin/BA3'], 'dirs' : ['bin', 'include'] } -- GitLab From 84b85cd3604256e9af2be975196276df1bf66c5c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 12:04:52 +0200 Subject: [PATCH 399/722] GSL dependency from 1.16 -> 2.1 --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb index fe8eabe029..3e9dc817b1 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -18,7 +18,7 @@ patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] dependencies = [ ('HTSlib', '1.3'), ('zlib', '1.2.8'), - ('GSL', '1.16'), + ('GSL', '2.1'), ] parallel = 1 -- GitLab From f8941af3095fdf106df4e80d4a7e56ee8d96fde2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 16:30:15 +0200 Subject: [PATCH 400/722] dos newlines to unix --- .../BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..c3ca739024 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.6.924' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.tar.gz' % version.replace('.', '-')] + +dependencies = [ + ('Perl', '5.22.1'), + ('DB_File', '1.835', versionsuffix), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' -- GitLab From 2d8bab7056a653924682ff0c75bed5b2b9eb77f9 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 16:57:19 +0200 Subject: [PATCH 401/722] DB_File for foss 2016a --- .../DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..b280622820 --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.835' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1'), + ('DB', '4.8.30'), +] + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From e65dfd7e88dc147706ce2f11c886b93549b6862e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 16:59:20 +0200 Subject: [PATCH 402/722] DB with foss 2016a --- .../easyconfigs/d/DB/DB-4.8.30-foss2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb new file mode 100644 index 0000000000..0db26d6d7e --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '4.8.30' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'tools' -- GitLab From 9c45c9617c8e9beeb9bf697457d644b33c664b3d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 17:02:48 +0200 Subject: [PATCH 403/722] biopython with foss 2016a --- .../Biopython-1.65-foss-2016a-2.7.11.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb new file mode 100644 index 0000000000..fc337c6c52 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = "PythonPackage" + +name = 'Biopython' +version = '1.65' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://biopython.org/DIST'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, + 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ + pyshortver), + 'lib/python%s/site-packages/BioSQL' % pyshortver] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' -- GitLab From f41070db77f5eec9d76f3d28e9ff2fbbab6cc607 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 13 Apr 2016 11:56:18 -0400 Subject: [PATCH 404/722] PGI: add easyconfig for version 16.3. --- .../p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..def0637f0b --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '16.3' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['618cb7ddbc57d4e4ed1f21a0ab25f427'] + +gccver = '4.9.3' +binutilsver = '2.25' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") + +moduleclass = 'compiler' -- GitLab From d4aba5b03e694f4e89d23260d4aaf6625dcb2c82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Apr 2016 18:53:09 +0200 Subject: [PATCH 405/722] fix bitstring 3.1.3 download URL --- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 6 ++++-- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 6 ++++-- .../easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb | 6 ++++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 6 ++++-- .../p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 6 ++++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 6 ++++-- 6 files changed, 24 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index b360b95e8c..51bd3f9ff0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -123,8 +123,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 2556554c13..80212964f1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -123,8 +123,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index 9c41844d2f..a99feb7078 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -126,8 +126,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index 3976e80bf2..bce00fd447 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -126,8 +126,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 62884700e2..0965b7d1e9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -128,8 +128,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 1ecb34bdf1..1468388148 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -126,8 +126,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], -- GitLab From ea5d4a30da2d8caaede51155c211321b3817f9c7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 21:06:48 +0200 Subject: [PATCH 406/722] buildopts added --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb index 3e9dc817b1..6d469bdd3b 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -25,6 +25,7 @@ parallel = 1 skipsteps = ['configure'] +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1' installopts = ' prefix=%(installdir)s' postinstallcmds = [ -- GitLab From 81be1a45da8cdbe335fe23b0a0a6cf396c8512d2 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 22:29:10 -0700 Subject: [PATCH 407/722] OptiX 3.8.0: fix easyconfig issues --- .../o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb index db096d2117..a4d1d070ca 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb @@ -3,6 +3,7 @@ # Authors:: Stephane Thiell ## easyblock = 'Binary' + name = 'OptiX' version = '3.8.0' @@ -13,21 +14,26 @@ description = """OptiX is NVIDIA SDK for easy ray tracing performance. toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} -#source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] - +# Registration required. Download links: +# https://developer.nvidia.com/designworks/optix/download +# https://developer.nvidia.com/designworks/optix/downloads/legacy sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.run'] checksums = [ 'ecf63cf32b87defa36d3cd283d085314', # NVIDIA-OptiX-SDK-3.8.0-linux64.run + '73eb689d6247e3d406cf3a38e80ec473', # NVIDIA-OptiX-SDK-3.7.0-linux64.run ] install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" sanity_check_paths = { - 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.so", "lib64/liboptixu.so"], + 'files': ["include/optix.h", + "include/optix_cuda.h", + "lib64/liboptix.%s" % SHLIB_EXT, + "lib64/liboptixu.%s" % SHLIB_EXT], 'dirs': [] } -modextravars = { 'OPTIX_HOME': '%(installdir)s' } +modextravars = {'OPTIX_HOME': '%(installdir)s'} moduleclass = 'vis' -- GitLab From 83165bc9263c9bd20569d013fda4c8b7c68a3711 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 22:29:41 -0700 Subject: [PATCH 408/722] add Nvidia OptiX 3.9.0 easyconfig --- .../o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..c8c1772071 --- /dev/null +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors:: Stephane Thiell +## +easyblock = 'Binary' + +name = 'OptiX' +version = '3.9.0' + +homepage = 'https://developer.nvidia.com/optix' +description = """OptiX is NVIDIA SDK for easy ray tracing performance. + It provides a simple framework for accessing the GPU’s massive ray tracing + power using state-of-the-art GPU algorithms.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +# Registration required. Download links: +# https://developer.nvidia.com/designworks/optix/download +# https://developer.nvidia.com/designworks/optix/downloads/legacy +sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.sh'] + +checksums = [ + '13b1953af766b82e0a4aaa28766a05a1', # NVIDIA-OptiX-SDK-3.9.0-linux64.sh +] + +install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ["include/optix.h", + "include/optix_cuda.h", + "lib64/liboptix.%s" % SHLIB_EXT, + "lib64/liboptixu.%s" % SHLIB_EXT], + 'dirs': [] +} + +modextravars = {'OPTIX_HOME': '%(installdir)s'} + +moduleclass = 'vis' -- GitLab From 0a8d27bcbf785078454859c00a483c64a99cd40b Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 22:54:42 -0700 Subject: [PATCH 409/722] add easyconfig for CUDA 7.0.28 --- easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb new file mode 100644 index 0000000000..e6b47b55c2 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -0,0 +1,18 @@ +name = 'CUDA' +version = '7.0.28' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux.run'] + +modextravars = {'CUDA_HOME': '%(installdir)s'} + +moduleclass = 'system' -- GitLab From e1f57b8fb0e64c025494208f50636c69c0cd6797 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 14 Apr 2016 07:25:03 +0100 Subject: [PATCH 410/722] Updates for limma, edgeR, Gviz, Rsubread --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 8 ++++---- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 60ddc2ec31..13ad83c774 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -62,7 +62,7 @@ exts_list = [ ('preprocessCore', '1.32.0', bioconductor_options), ('affy', '1.48.0', bioconductor_options), ('GO.db', '3.2.2', bioconductor_options), - ('limma', '3.26.8', bioconductor_options), + ('limma', '3.26.9', bioconductor_options), ('RBGL', '1.46.0', bioconductor_options), ('org.Hs.eg.db', '3.2.3', bioconductor_options), ('AnnotationForge', '1.12.2', bioconductor_options), @@ -70,7 +70,7 @@ exts_list = [ ('annaffy', '1.42.0', bioconductor_options), ('gcrma', '2.42.0', bioconductor_options), ('oligoClasses', '1.32.0', bioconductor_options), - ('edgeR', '3.12.0', bioconductor_options), + ('edgeR', '3.12.1', bioconductor_options), ('PFAM.db', '3.2.2', bioconductor_options), ('perm', '1.0-0.0', ext_options), ('baySeq', '2.4.1', bioconductor_options), @@ -126,13 +126,13 @@ exts_list = [ ('Mfuzz', '2.30.0', bioconductor_options), ('maSigPro', '1.42.0', bioconductor_options), ('SPIA', '2.22.0', bioconductor_options), - ('Gviz', '1.14.4', bioconductor_options), + ('Gviz', '1.14.7', bioconductor_options), ('cummeRbund', '2.12.1', bioconductor_options), ('GenomicFiles', '1.6.2', bioconductor_options), ('derfinderHelper', '1.4.1', bioconductor_options), ('derfinder', '1.4.4', bioconductor_options), ('polyester', '1.6.0', bioconductor_options), - ('Rsubread', '1.20.3', bioconductor_options), + ('Rsubread', '1.20.5', bioconductor_options), ('pcaMethods', '1.60.0', bioconductor_options), ('marray', '1.48.0', bioconductor_options), ('CGHbase', '1.30.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index 75d2568589..64a35be205 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -61,7 +61,7 @@ exts_list = [ ('preprocessCore', '1.32.0', bioconductor_options), ('affy', '1.48.0', bioconductor_options), ('GO.db', '3.2.2', bioconductor_options), - ('limma', '3.26.8', bioconductor_options), + ('limma', '3.26.9', bioconductor_options), ('RBGL', '1.46.0', bioconductor_options), ('org.Hs.eg.db', '3.2.3', bioconductor_options), ('AnnotationForge', '1.12.2', bioconductor_options), @@ -69,7 +69,7 @@ exts_list = [ ('annaffy', '1.42.0', bioconductor_options), ('gcrma', '2.42.0', bioconductor_options), ('oligoClasses', '1.32.0', bioconductor_options), - ('edgeR', '3.12.0', bioconductor_options), + ('edgeR', '3.12.1', bioconductor_options), ('PFAM.db', '3.2.2', bioconductor_options), ('perm', '1.0-0.0', ext_options), ('baySeq', '2.4.1', bioconductor_options), @@ -125,13 +125,13 @@ exts_list = [ ('Mfuzz', '2.30.0', bioconductor_options), ('maSigPro', '1.42.0', bioconductor_options), ('SPIA', '2.22.0', bioconductor_options), - ('Gviz', '1.14.4', bioconductor_options), + ('Gviz', '1.14.7', bioconductor_options), ('cummeRbund', '2.12.1', bioconductor_options), ('GenomicFiles', '1.6.2', bioconductor_options), ('derfinderHelper', '1.4.1', bioconductor_options), ('derfinder', '1.4.4', bioconductor_options), ('polyester', '1.6.0', bioconductor_options), - ('Rsubread', '1.20.3', bioconductor_options), + ('Rsubread', '1.20.5', bioconductor_options), ('pcaMethods', '1.60.0', bioconductor_options), ('marray', '1.48.0', bioconductor_options), ('CGHbase', '1.30.0', bioconductor_options), -- GitLab From 52f5d1c9486f961db52a9ec2ff4373b760e0d539 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 23:34:11 -0700 Subject: [PATCH 411/722] add easyconfig for cuDNN 4.0 and 5.0 --- easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb | 32 ++++++++++++++++++++++ easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb | 32 ++++++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb new file mode 100644 index 0000000000..5bcd0e1aa3 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '4.0' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-7.0-linux-x64-v%(version)s-prod.tgz'] + +dependencies = [('CUDA', '7.5.18')] + +checksums = [ + '845ead4b37f1a2a243d7d1b4d42d1d8b', # cudnn-7.0-linux-x64-v4.0-prod.tgz +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb new file mode 100644 index 0000000000..fcf816c8fb --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '5.0' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-7.5-linux-x64-v%(version)s-rc.tgz'] + +dependencies = [('CUDA', '7.5.18')] + +checksums = [ + '0febee3f11276218668857191514b7e0', # cudnn-7.5-linux-x64-v5.0-rc.tgz +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' -- GitLab From 0de0c65aa8aee81d2dbb094481227bf4976ca9dd Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 23:52:00 -0700 Subject: [PATCH 412/722] OptiX: fix a few issues --- easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb | 5 +---- easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb | 4 +--- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb index a4d1d070ca..69dec5c347 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb @@ -21,15 +21,12 @@ sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.run'] checksums = [ 'ecf63cf32b87defa36d3cd283d085314', # NVIDIA-OptiX-SDK-3.8.0-linux64.run - '73eb689d6247e3d406cf3a38e80ec473', # NVIDIA-OptiX-SDK-3.7.0-linux64.run ] install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" sanity_check_paths = { - 'files': ["include/optix.h", - "include/optix_cuda.h", - "lib64/liboptix.%s" % SHLIB_EXT, + 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.%s" % SHLIB_EXT, "lib64/liboptixu.%s" % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb index c8c1772071..7960265e87 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb @@ -26,9 +26,7 @@ checksums = [ install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" sanity_check_paths = { - 'files': ["include/optix.h", - "include/optix_cuda.h", - "lib64/liboptix.%s" % SHLIB_EXT, + 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.%s" % SHLIB_EXT, "lib64/liboptixu.%s" % SHLIB_EXT], 'dirs': [] } -- GitLab From 278865b55584db402d5cbe24ffd599c6b90a0d0e Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 23:59:34 -0700 Subject: [PATCH 413/722] remove CUDA_HOME modext as it is already handled by easyblock --- easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb index e6b47b55c2..87e535776e 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -13,6 +13,4 @@ source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_majo sources = ['%(namelower)s_%(version)s_linux.run'] -modextravars = {'CUDA_HOME': '%(installdir)s'} - moduleclass = 'system' -- GitLab From 4a4426f75304e17e6e10c50200e4527aa4f8fd32 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 09:37:21 +0200 Subject: [PATCH 414/722] Add ALPS --- .../ALPS-2.2b4-intel-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..27a5876ff2 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'ALPS' +version = '2.2b4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.example.com' +description = """ The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort +aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ +libraries for simplifying the development of such code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://alps.comp-phys.org/static/software/releases'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('HDF5', '1.8.16'), + ('matplotlib', '1.5.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'phys' -- GitLab From c972ef56ffd0e56fa124971f5ef54666cf5b5bae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 10:16:24 +0200 Subject: [PATCH 415/722] add easyconfig Perl-5.20.3-intel-2015a.eb --- .../p/Perl/Perl-5.20.3-intel-2015a.eb | 909 ++++++++++++++++++ 1 file changed, 909 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb new file mode 100644 index 0000000000..e4d3b47d6f --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb @@ -0,0 +1,909 @@ +name = 'Perl' +version = '5.20.3' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.58', { + 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('TAP::Harness::Env', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.021', { + 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '0.46', { + 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.93', { + 'source_tmpl': 'DateTime-TimeZone-1.93.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.22', { + 'source_tmpl': 'Try-Tiny-0.22.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Params::Validate', '1.21', { + 'source_tmpl': 'Params-Validate-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.20', { + 'source_tmpl': 'DateTime-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Module::Build', '0.4214', { + 'source_tmpl': 'Module-Build-0.4214.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Readonly', '2.00', { + 'source_tmpl': 'Readonly-2.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.27', { + 'source_tmpl': 'Tree-DAG_Node-1.27.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.48', { + 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.72', { + 'source_tmpl': 'Shell-0.72.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.47', { + 'source_tmpl': 'PathTools-3.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::WrapTie', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.40', { + 'source_tmpl': 'Test-Exception-0.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.11', { + 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.69', { + 'source_tmpl': 'URI-1.69.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.00', { + 'source_tmpl': 'Pod-POM-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.43', { + 'source_tmpl': 'Text-Diff-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.020', { + 'source_tmpl': 'IO-Socket-SSL-2.020.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Getopt::Long', '2.47', { + 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '0.117', { + 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.000002', { + 'source_tmpl': 'Moo-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.05', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.63', { + 'source_tmpl': 'Test-Differences-0.63.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.14', { + 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9912', { + 'source_tmpl': 'version-0.9912.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD/'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.30', { + 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.11', { + 'source_tmpl': 'AnyEvent-7.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0609', { + 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::Tester', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967012', { + 'source_tmpl': 'Parse-RecDescent-1.967012.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.36', { + 'source_tmpl': 'Carp-1.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.13', { + 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT'], + }), + ('Capture::Tiny', '0.30', { + 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('LWP', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000001', { + 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.19', { + 'source_tmpl': 'File-Which-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.39', { + 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.42', { + 'source_tmpl': 'Scalar-List-Utils-1.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('IO::Scalar', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.87', { + 'source_tmpl': 'Log-Handler-0.87.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Devel::StackTrace', '2.00', { + 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1603', { + 'source_tmpl': 'Moose-2.1603.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.33', { + 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9154', { + 'source_tmpl': 'CPANPLUS-0.9154.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Harness', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.04', { + 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.14', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' -- GitLab From 5baa6d14a4f0a16626d4317e433b63f618984f40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 10:22:07 +0200 Subject: [PATCH 416/722] fix Perl dependency in worker, it required non-standard Perl modules --- easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index e3023d8f2c..cdf0174497 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('Perl', '5.20.1', '-bare') + ('Perl', '5.20.3') ] # adjust worker configuration file -- GitLab From c8354ece8ecb261c40e561951d32c1d0c002684f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 13:10:24 +0200 Subject: [PATCH 417/722] add easyconfig dask-0.8.2-intel-2016a-Python-2.7.11.eb --- .../dask-0.8.2-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..10a9f3bf36 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From 15df4db6a6f422c44e7f33a2f203776aca51fd47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 13:16:45 +0200 Subject: [PATCH 418/722] add easyconfig dask-0.8.2-intel-2016a-Python-3.5.1.eb --- .../dask-0.8.2-intel-2016a-Python-3.5.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..7dcf741ab4 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From a34e72227fe18a01ef50128de64d8b9dd7aab7ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 13:41:02 +0200 Subject: [PATCH 419/722] add easyconfig worker-1.6.4-intel-2016a.eb --- .../w/worker/worker-1.6.4-intel-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb new file mode 100644 index 0000000000..3c373e597a --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.4' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.22.1') +] + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', # tweak this (maybe) + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', # tweak this (maybe) +] + +moduleclass = 'tools' -- GitLab From 942d3126ede0f528f12f643439eab5b7d96d7043 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 14:35:01 +0200 Subject: [PATCH 420/722] add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma --- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 1 + easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index 782d02fe62..c11711336f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), + ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index 5dcd8c848b..f0600eefc0 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), + ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -- GitLab From c9dd68acf5e40c1f285cc47073077135a7c24887 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 14 Apr 2016 08:38:54 -0400 Subject: [PATCH 421/722] PGI: adjust license file (suggested by @boegel) and add numactl-GCCcore dependency. --- .../n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb | 25 +++++++++++++++++++ .../p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb | 4 +-- 2 files changed, 27 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..e54c32859f --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('binutils', '2.25')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb index def0637f0b..1b4b9a4866 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb @@ -16,10 +16,10 @@ versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ ('GCCcore', gccver), ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), ] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") +license_file = HOME + '/licenses/pgi/license.dat' moduleclass = 'compiler' -- GitLab From e913f23e064c6018bcd09084aebc10d61b54e7ea Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 14:51:53 +0200 Subject: [PATCH 422/722] Almost there for ALPS --- ...1.eb => ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb} | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/a/ALPS/{ALPS-2.2b4-intel-2016a-Python-2.7.11.eb => ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb} (73%) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb similarity index 73% rename from easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb index 27a5876ff2..cf98c0aae4 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'ALPS' -version = '2.2b4' +version = '2.2.b4' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.example.com' @@ -17,12 +17,20 @@ source_urls = ['http://alps.comp-phys.org/static/software/releases'] builddependencies = [('CMake', '3.4.3')] dependencies = [ + ('zlib', '1.2.8'), ('Python', '2.7.11'), - ('Boost', '1.60.0', versionsuffix), + ('Boost', '1.58.0', versionsuffix), ('HDF5', '1.8.16'), ('matplotlib', '1.5.1', versionsuffix), ] +configopts = '-DSZIP_INCLUDE_DIR=$EBROOTSZIP/include -DSZIP_LIBRARY=$EBROOTSZIP/lib ' +configopts += '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' + +separate_build_dir = True + +maxparallel = 1 + sanity_check_paths = { 'files': [], 'dirs': ["."] -- GitLab From 8e87dab94667a21f1e994e7548b7bfc681751c91 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:12:02 +0200 Subject: [PATCH 423/722] Add Boost 1.58 for intel/2016a --- .../Boost-1.58.0-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f392ae7ad4 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.58.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From e9dedd35e4fdb96140766e12e25dc1be849b8708 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:35:32 +0200 Subject: [PATCH 424/722] Add MariaDB 10.1.13 --- .../j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 23 +++++++++++++++ .../m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 29 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb new file mode 100644 index 0000000000..76daf74962 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.1.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.canonware.com/download/jemalloc/'] +sources = [SOURCE_TAR_BZ2] + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.1']} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb new file mode 100644 index 0000000000..e373db06bd --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.1.13' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('ncurses', '6.0'), + ('jemalloc', '4.1.0'), +] + +builddependencies = [('CMake', '3.4.3')] + +#configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'data' -- GitLab From f1eefdcb7cbdca66815ced46a8c94986afd8e219 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:37:25 +0200 Subject: [PATCH 425/722] jemalloc: use github --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 76daf74962..840d6b9d2e 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -9,8 +9,8 @@ description = """jemalloc is a general purpose malloc(3) implementation that emp toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://www.canonware.com/download/jemalloc/'] -sources = [SOURCE_TAR_BZ2] +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] sanity_check_paths = { 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, -- GitLab From 9b6344d8e154a27ab11b607c9fe36330c4c4d291 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:44:15 +0200 Subject: [PATCH 426/722] Use autogen for jemalloc --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 840d6b9d2e..26a2f81a65 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://github.com/jemalloc/jemalloc/archive'] sources = ['%(version)s.tar.gz'] +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " + sanity_check_paths = { 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], -- GitLab From 57391a12530ca3fde36656478ed248ed9ecd0b3f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:49:35 +0200 Subject: [PATCH 427/722] Fix jemalloc build --- easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 26a2f81a65..59c52ac8e4 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -15,6 +15,7 @@ sources = ['%(version)s.tar.gz'] builddependencies = [('Autotools', '20150215')] preconfigopts = "./autogen.sh && " +prebuildopts = "make dist && " sanity_check_paths = { 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, -- GitLab From 87d301508772d255d769f48a01cc79b066c30236 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:53:00 +0200 Subject: [PATCH 428/722] Fix sanity check of jemalloc --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 59c52ac8e4..e13485c431 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -18,11 +18,11 @@ preconfigopts = "./autogen.sh && " prebuildopts = "make dist && " sanity_check_paths = { - 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, - 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'lib/libjemalloc.so.2', 'include/jemalloc/jemalloc.h'], 'dirs': ['share'], } -modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.1']} +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.2']} moduleclass = 'lib' -- GitLab From 494835b0f6103687cafe2ccb67e54767058a8651 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 16:20:47 +0200 Subject: [PATCH 429/722] Add options to MariaDB --- .../easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index e373db06bd..dc6e52c840 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -15,11 +15,13 @@ dependencies = [ ('zlib', '1.2.8'), ('ncurses', '6.0'), ('jemalloc', '4.1.0'), + ('PCRE', '8.38'), + ('XZ', '5.2.2'), ] builddependencies = [('CMake', '3.4.3')] -#configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DWITH_INNODB_LZMA=on" sanity_check_paths = { 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], -- GitLab From b1e18a3183cb74b9ad3de414a1610cadfb7a7f98 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 16:54:14 +0200 Subject: [PATCH 430/722] Even more deps for MariaDB --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index dc6e52c840..68f736cb1a 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -17,6 +17,8 @@ dependencies = [ ('jemalloc', '4.1.0'), ('PCRE', '8.38'), ('XZ', '5.2.2'), + ('Boost', '1.60.0'), + ('libxml2', '2.9.3'), ] builddependencies = [('CMake', '3.4.3')] -- GitLab From e8ddbaeb437dc2dd0d5f91184e5872522e2a5aee Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 17:37:34 +0200 Subject: [PATCH 431/722] Add PostgreSQL 9.5.2 --- .../PostgreSQL-9.5.2-intel-2016a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb new file mode 100644 index 0000000000..eef652753d --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.5.2' + +homepage = 'http://www.mysql.com/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +java = 'Java' +javaver = '1.8.0_77' + +dependencies = [ + (java, javaver, '', True), + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.22.1'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 2c9d18f3b8b4ad7726e68f266d51a22177c755d5 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Thu, 14 Apr 2016 10:21:58 -0700 Subject: [PATCH 432/722] Fix source_urls for CUDA 7.0.28 --- easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb index 87e535776e..ab24e09cd3 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -9,7 +9,9 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] +source_urls = [ + 'http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/Prod/local_installers/', +] sources = ['%(namelower)s_%(version)s_linux.run'] -- GitLab From bb3faf23369c5cb5c69f998022a92109f0a88487 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Thu, 14 Apr 2016 10:42:39 -0700 Subject: [PATCH 433/722] cuDNN: use 5.0-rc instead of 5.0 (RC version) --- .../easyconfigs/c/cuDNN/{cuDNN-5.0.eb => cuDNN-5.0-rc.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/cuDNN/{cuDNN-5.0.eb => cuDNN-5.0-rc.eb} (91%) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb similarity index 91% rename from easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb rename to easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb index fcf816c8fb..536c2f33c6 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb @@ -6,7 +6,7 @@ easyblock = 'Tarball' name = 'cuDNN' -version = '5.0' +version = '5.0-rc' homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for @@ -16,7 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download -sources = ['%(namelower)s-7.5-linux-x64-v%(version)s-rc.tgz'] +sources = ['%(namelower)s-7.5-linux-x64-v%(version)s.tgz'] dependencies = [('CUDA', '7.5.18')] -- GitLab From 08549d2371151ec00e4332545557bbc407b77f12 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 15 Apr 2016 14:12:41 +1200 Subject: [PATCH 434/722] Added zlib configopt per request --- easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb index 7c1a817fb6..59e0331739 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [ ('zlib', '1.2.8'), -- GitLab From a97102970f055a0393f3c52d072bd3f55aed02cc Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 15 Apr 2016 16:47:05 +1200 Subject: [PATCH 435/722] Update checksum --- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 3ea34a9824..99e680c26d 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -14,8 +14,10 @@ source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] # tarballs with the same version number can have different checksums. For this # reason, it is suggested to manually download and rename the tarball. The # checksum may also need updating from time to time. +# Checksum last updated: 15 April 2016 +# Date tarball was reported to have been modified: 11 January 2016 sources = ['dftd3-%(version)s.tgz'] -checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] +checksums = [('md5', 'c9d6a92c43bb2ba71ad75f388fdce216')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From cffac5f722257a77ce6ef8b6a705c3f67ab81d8e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 15 Apr 2016 13:03:39 +0800 Subject: [PATCH 436/722] files generated with "eb Python-2.7.11-intel-2016a.eb --try-toolchain=intel,2016.02-GCC-4.9 -r" --- .../Autoconf-2.69-intel-2016.02-GCC-4.9.eb | 26 ++++ .../Automake-1.15-intel-2016.02-GCC-4.9.eb | 33 +++++ ...utotools-20150215-intel-2016.02-GCC-4.9.eb | 17 +++ .../bzip2-1.0.6-intel-2016.02-GCC-4.9.eb | 15 ++ .../g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb | 30 ++++ .../libreadline-6.3-intel-2016.02-GCC-4.9.eb | 30 ++++ .../libtool-2.4.6-intel-2016.02-GCC-4.9.eb | 17 +++ .../m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb | 23 +++ .../ncurses-6.0-intel-2016.02-GCC-4.9.eb | 34 +++++ .../Python-2.7.11-intel-2016.02-GCC-4.9.eb | 139 ++++++++++++++++++ .../SQLite-3.9.2-intel-2016.02-GCC-4.9.eb | 40 +++++ .../t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb | 25 ++++ .../Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb | 26 ++++ .../zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb | 22 +++ 14 files changed, 477 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..e627b672b4 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..84750fffa9 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..65fd1e93a3 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..d048641ea5 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..70b7019537 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..c3f437ac8a --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..857c0faabb --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..b3bc79e1fe --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..7c1c8c34c6 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..b8a12d273e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,139 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%s-sse42.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..3555a7ac4c --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..c2af97cc03 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb new file mode 100644 index 0000000000..ed76be27b6 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..a389aa72f5 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From e43d75237ef71c7f231673f9c189e1bdafdf0fcf Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 15 Apr 2016 13:11:17 +0800 Subject: [PATCH 437/722] adapted from ASE-3.9.1.4567-intel-2016a-Python-2.7.11.eb --- ...0.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb new file mode 100644 index 0000000000..95f2c7f4a5 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.10.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase/' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ['https://pypi.python.org/packages/source/a/ase/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], +} + +moduleclass = 'chem' -- GitLab From 213c16a9d14446e594d1873b334a7427e51dcf0f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 15 Apr 2016 11:40:36 +0200 Subject: [PATCH 438/722] DB-6.2.23 for foss 2016a --- .../easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb new file mode 100644 index 0000000000..fcf1bd7696 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '6.2.23' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["include/db.h"], + 'dirs': [], +} + +moduleclass = 'tools' \ No newline at end of file -- GitLab From 5561b2936134e5e5c2583218364d104f37419971 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 15 Apr 2016 11:46:08 +0200 Subject: [PATCH 439/722] Drop java and add Python suffix to PostgreSQL --- ...016a.eb => PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb} | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) rename easybuild/easyconfigs/p/PostgreSQL/{PostgreSQL-9.5.2-intel-2016a.eb => PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb} (95%) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb similarity index 95% rename from easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb rename to easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index eef652753d..a7590c6580 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'PostgreSQL' version = '9.5.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.mysql.com/' description = """PostgreSQL is a powerful, open source object-relational database system. @@ -20,11 +21,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} osdependencies = [('openssl-devel', 'libssl-dev')] -java = 'Java' -javaver = '1.8.0_77' - dependencies = [ - (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), -- GitLab From 9c90718ca8b5ffefc190be503c2e997aeead2c5b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 15 Apr 2016 12:09:27 +0200 Subject: [PATCH 440/722] Added MADlib --- .../MADlib-1.9-intel-2016a-Python-2.7.11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..35ae5d23c5 --- /dev/null +++ b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'MADlib' +version = '1.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://madlib.incubator.apache.org' +description = """MADlib: Big Data Machine Learning in SQL for Data Scientists""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['apache-madlib-%(version)s-incubating-source.tar.gz'] +source_urls = ['https://dist.apache.org/repos/dist/release/incubator/madlib/%(version)s-incubating'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('Python', '2.7.11'), + ('PostgreSQL', '9.5.2', versionsuffix), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/madpack'], + 'dirs': [] +} + +moduleclass = 'data' -- GitLab From f0a0f612b846ea753245c4d73fc78f0ea1325c99 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 15 Apr 2016 13:52:48 +0200 Subject: [PATCH 441/722] Biopython with foss 2016a --- ...Biopython-1.65-foss-2016a-Python-2.7.11.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..fc337c6c52 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = "PythonPackage" + +name = 'Biopython' +version = '1.65' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://biopython.org/DIST'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, + 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ + pyshortver), + 'lib/python%s/site-packages/BioSQL' % pyshortver] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' -- GitLab From 55e6a328a624cb037bf7a70e9d70fe3e2d8982a2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 15 Apr 2016 14:15:34 +0200 Subject: [PATCH 442/722] numpy dependency --- .../b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index fc337c6c52..8730db898f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -30,6 +30,7 @@ versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ (python, pyver), + ('numpy', '1.10.1', versionsuffix) ] sanity_check_paths = { -- GitLab From 9e097a1ed69abae68f558a85caa3128c44b78077 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 14:42:37 +0200 Subject: [PATCH 443/722] add easyconfig ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb, add easyconfig freetype-2.6.3-intel-2016a.eb --- .../f/freetype/freetype-2.6.3-intel-2016a.eb | 22 ++++++++ ...ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 55 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb new file mode 100644 index 0000000000..6245460dc2 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.3' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..2cea64ddb8 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,55 @@ +name = 'ROOT' +version = 'v5.34.36' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', + 'ROOT-v5.34.26_libX.patch', +] + +dependencies = [ + ('GSL', '2.1'), + ('Mesa', '11.1.2'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), + ('CFITSIO', '3.38'), + ('freetype', '2.6.3'), + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('libXft', '2.3.2'), + ('libXpm', '3.5.11'), + ('libXext', '1.3.3'), +] + +# use external ZLIB +preconfigopts = 'env ZLIB=$EBROOTZLIB ' + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xrootd --disable-mysql --disable-krb5 --disable-odbc ' +configopts += ' --disable-oracle --disable-pgsql --disable-qt --disable-sqlite' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +configopts += ' --with-cfitsio-incdir=$EBROOTCFITSIO/include --with-cfitsio-libdir=$EBROOTCFITSIO/lib' +configopts += ' --with-opengl-incdir=$EBROOTMESA/include --with-opengl-libdir=$EBROOTMESA/lib' +configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLIBXEXT/lib' +configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' +configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' + +moduleclass = 'data' -- GitLab From 523361945d9181f98ac685afa9cebcd16a0644bb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 14:46:28 +0200 Subject: [PATCH 444/722] modernise libxml2 2.9.1 easyconfig --- .../l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb index d68ae2eaee..ae7f22f7a4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -13,15 +14,11 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' - -pythonver = '2.7.5' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.5'), ] moduleclass = 'lib' -- GitLab From 1ac2352b2d011c437af9827b9518b29f661e467e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 14:55:52 +0200 Subject: [PATCH 445/722] downgrade back to freetype 2.9.3 due to conflicts in dep graph --- .../r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb index 2cea64ddb8..7d1106317b 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ dependencies = [ ('libxml2', '2.9.3'), ('PCRE', '8.38'), ('CFITSIO', '3.38'), - ('freetype', '2.6.3'), + ('freetype', '2.6.2'), ('Python', '2.7.11'), ('zlib', '1.2.8'), ('libXft', '2.3.2'), -- GitLab From 88eb3bb5814e86288fa54bc8ab85b04733c72eea Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 15 Apr 2016 09:02:06 -0400 Subject: [PATCH 446/722] PGI: add OpenMPI and pompi toolchain easyconfigs. --- .../OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 40 +++++++++++++++++++ .../easyconfigs/p/pompi/pompi-2016.03.eb | 19 +++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/p/pompi/pompi-2016.03.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..8cd6dea646 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify + +dependencies = [('hwloc', '1.11.2')] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +#sanity_check_commands = [ +# ('mpicc --version | grep pgcc', ''), +# ('mpicxx --version | grep pgc++', ''), +# ('mpifort --version | grep pgfortran', ''), +#] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb b/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb new file mode 100644 index 0000000000..0bf9bb7552 --- /dev/null +++ b/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'pompi' +version = '2016.03' +pgisuffix = '-GCC-4.9.3-2.25' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.3' + +dependencies = [ + ('PGI', compver, pgisuffix), + ('OpenMPI', '1.10.2', '', ('PGI', '%s%s' % (compver, pgisuffix))), +] + +moduleclass = 'toolchain' -- GitLab From a6b0c16f90bac68dbde7a849e551b15cce6130cb Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 15 Apr 2016 09:57:14 -0400 Subject: [PATCH 447/722] PGI: add pomkl-2016.03 toolchain + imkl-11.3.2.181-pompi + HPL --- .../h/HPL/HPL-2.1-pomkl-2016.03.eb | 23 ++++++++++++ .../i/imkl/imkl-11.3.2.181-pompi-2016.03.eb | 36 +++++++++++++++++++ .../easyconfigs/p/pomkl/pomkl-2016.03.eb | 20 +++++++++++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb create mode 100644 easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb new file mode 100644 index 0000000000..73bc06cddb --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb @@ -0,0 +1,23 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'pomkl', 'version': '2016.03'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +# needs to include -ldl or else we get +# .../libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' +import os +os.environ['LIBS'] = '-ldl' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb new file mode 100644 index 0000000000..ac3a95728c --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.2.181' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'pompi', 'version': '2016.03'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb b/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb new file mode 100644 index 0000000000..6b7d80bf52 --- /dev/null +++ b/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'pomkl' +version = '2016.03' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.3' +gccsuff = '-GCC-4.9.3-2.25' + +dependencies = [ + ('PGI', compver, gccsuff), + ('OpenMPI', '1.10.2', '', ('PGI', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.2.181', '', ('pompi', '%s' % (version))), +] + +moduleclass = 'toolchain' -- GitLab From dc578361e24586f76539339d6624d11163d73cfb Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 15 Apr 2016 10:27:01 -0400 Subject: [PATCH 448/722] Move checksum under sources. --- .../easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb index e54c32859f..91b7fa73b1 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb @@ -3,8 +3,6 @@ easyblock = 'ConfigureMake' name = 'numactl' version = '2.0.11' -checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] - homepage = 'http://oss.sgi.com/projects/libnuma/' description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. @@ -15,6 +13,8 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] sources = [SOURCE_TAR_GZ] +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + builddependencies = [('binutils', '2.25')] sanity_check_paths = { -- GitLab From 63e171985e5db8c4347f3689c19e473fb2302667 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 22:34:37 +0200 Subject: [PATCH 449/722] add easyconfig Singularity-1.0-GCC-4.9.3-2.25.eb --- .../Singularity-1.0-GCC-4.9.3-2.25.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..8d785f5395 --- /dev/null +++ b/easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Singularity' +version = '1.0' + +homepage = 'http://gmkurtzer.github.io/singularity' +description = """Singularity is a portable application stack packaging and runtime utility.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/sapprun', 'bin/singularity'], + 'dirs': ['libexec/singularity'], +} + +moduleclass = 'tools' -- GitLab From ea458d6c6e4761e35835c3a85f1b25894dc9eab0 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:54:18 +0800 Subject: [PATCH 450/722] add CPPFLAGS=-fgnu89-inline to M4 eb --- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb index b3bc79e1fe..899804b18f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 2a5b19d02f135381c0d70b5bddb092400cc9a867 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:55:24 +0800 Subject: [PATCH 451/722] use env in libreadline eb --- .../l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb index c3f437ac8a..9c5b9b6279 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + -- GitLab From 21ad457a50367bae49fcabae0713cddf08c4fcfa Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 08:01:55 +0800 Subject: [PATCH 452/722] use pyver template --- .../ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 95f2c7f4a5..3592b22134 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'ASE' version = '3.10.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://wiki.fysik.dtu.dk/ase/' description = """ASE is a python package providing an open source Atomic Simulation Environment @@ -12,17 +13,15 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = ['https://pypi.python.org/packages/source/a/ase/'] sources = ['%(namelower)s-%(version)s.tar.gz'] -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ] sanity_check_paths = { 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], - 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } moduleclass = 'chem' -- GitLab From 4a9dbd98c864d90586d41615b289cb2b617d348d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 08:03:41 +0800 Subject: [PATCH 453/722] use PYPI_LOWER_SOURCE and SOURCELOWER_TAR_GZ --- .../a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 3592b22134..96dd7193cd 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -10,8 +10,8 @@ description = """ASE is a python package providing an open source Atomic Simulat toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -source_urls = ['https://pypi.python.org/packages/source/a/ase/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] versionsuffix = '-Python-%s' % pyver -- GitLab From 559166337d94b390123c8fd3858e990479bb3851 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 08:05:29 +0800 Subject: [PATCH 454/722] remove duplicated versionsuffix --- .../a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 96dd7193cd..ca4b5697db 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -13,8 +13,6 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -versionsuffix = '-Python-%s' % pyver - dependencies = [ ('Python', '2.7.11'), ] -- GitLab From d9bbb9563527681c5ae947bd520e25ff1cadf9ea Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 16 Apr 2016 17:42:07 +0200 Subject: [PATCH 455/722] Fix packmol eb and add newest version --- .../p/packmol/packmol-13.243-ictce-4.1.13.eb | 4 ++-- .../p/packmol/packmol-16.103-intel-2016a.eb | 23 +++++++++++++++++++ 2 files changed, 25 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb b/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb index 29c565eb8d..669406175c 100644 --- a/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb @@ -3,13 +3,13 @@ easyblock = "MakeCp" name = 'packmol' version = '13.243' -homepage = 'http://www.cmbi.ru.nl/molden/' +homepage = 'http://www.ime.unicamp.br/~martinez/packmol/' description = "Packing Optimization for Molecular Dynamics Simulations" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['https://packmol.googlecode.com/files'] +source_urls = ['http://leandro.iqm.unicamp.br/packmol/versionhistory'] buildopts = 'FORTRAN="$F90"' diff --git a/easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb b/easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb new file mode 100644 index 0000000000..a5ed58eedd --- /dev/null +++ b/easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = "MakeCp" + +name = 'packmol' +version = '16.103' + +homepage = 'http://www.ime.unicamp.br/~martinez/packmol/' +description = "Packing Optimization for Molecular Dynamics Simulations" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://leandro.iqm.unicamp.br/packmol/versionhistory'] + +buildopts = 'FORTRAN="$F90"' + +files_to_copy = [(['packmol'], 'bin'), 'COPYING', 'AUTHORS', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/packmol', 'COPYING', 'AUTHORS', 'LICENSE'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 2bd9fac7ab90a4cb83e0a5c77cfd85273eb56e91 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Sat, 16 Apr 2016 14:11:16 -0400 Subject: [PATCH 456/722] Using %(pyver)s and %(pyshortver)s template for ScientificPython and numpy easyconfig --- .../n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb | 8 +++----- .../ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb | 9 +++------ 2 files changed, 6 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb index e591de8fe1..eeb3a0e326 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb @@ -13,14 +13,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['numpy-1.8.1-mkl.patch'] +versionsuffix = '-Python-%(pyver)s' -python = 'Python' -pyver = '2.7.11' -versionsuffix = '-%s-%s' % (python, pyver) +patches = ['numpy-1.8.1-mkl.patch'] dependencies = [ - (python, pyver), + ('Python', '2.7.11'), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index ef29eaf445..c1b4e8f39a 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -13,13 +13,10 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = '-Python-%s' % pyver +versionsuffix = '-Python-%(pyver)s' dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), # older version of numpy than the one included in Python module required # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for ('numpy', '1.8.2', versionsuffix), @@ -29,7 +26,7 @@ options = {'modulename': 'Scientific'} sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/Scientific' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Scientific'], } moduleclass = 'math' -- GitLab From ee958027b6ebcc5c2ee4a0161c16e773e52aa5f9 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Sat, 16 Apr 2016 15:02:52 -0400 Subject: [PATCH 457/722] adjust position versionsuffix --- .../n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb | 3 +-- .../ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb index eeb3a0e326..b9ddbc1927 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'numpy' version = '1.8.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.numpy.org' description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: @@ -13,8 +14,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' - patches = ['numpy-1.8.1-mkl.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index c1b4e8f39a..1c40ab4f4d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'ScientificPython' version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://sourcesup.cru.fr/projects/scientific-py/' description = """ScientificPython is a collection of Python modules for scientific computing. @@ -13,7 +14,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' dependencies = [ ('Python', '2.7.11'), -- GitLab From f2412f0594a35ca854a7aa07266a8278ef60fb4a Mon Sep 17 00:00:00 2001 From: jrbosch Date: Sat, 16 Apr 2016 15:05:37 -0400 Subject: [PATCH 458/722] Update ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb --- .../ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index 1c40ab4f4d..267282ee97 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -14,7 +14,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.11'), # older version of numpy than the one included in Python module required -- GitLab From 7f3237cc029b0d1f089f80a06e6f764807f8e8f7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 17 Apr 2016 16:16:22 +0200 Subject: [PATCH 459/722] preinstall opts --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index b280622820..efd22bd922 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -3,6 +3,9 @@ easyblock = 'PerlModule' name = 'DB_File' version = '1.835' versionsuffix = '-Perl-%(perlver)s' +preinstallopts = 'export DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib' + + homepage = 'http://perldoc.perl.org/DB_File.html' description = """Perl5 access to Berkeley DB version 1.x.""" @@ -14,7 +17,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Perl', '5.22.1'), - ('DB', '4.8.30'), + ('DB', '6.2.23'), ] sanity_check_paths = { -- GitLab From b2ba3820d14534216925834905539bb6153994b9 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 17 Apr 2016 17:25:37 +0200 Subject: [PATCH 460/722] Bowtie with foss 2016a --- .../b/Bowtie/Bowtie-1.1.2-foss-2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..7979ba4e23 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb @@ -0,0 +1,18 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +moduleclass = 'bio' -- GitLab From 0e80dac7141e79a117e7674230156c9f66204fc1 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 12:36:43 +1200 Subject: [PATCH 461/722] New EasyConfig for binutils 2.26 with the GCC core 4.9.2 --- .../b/binutils/binutils-2.26-GCCcore-4.9.2.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..75c194bc7b --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c6e1b054ff4644003954ba0dbe6ac7dab8a525d9 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:25:07 +1200 Subject: [PATCH 462/722] New EasyConfig for binutils 2.25 with GCC core 4.9.2 --- .../b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..a9d4815d89 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From a0283d931e8b0133cca0e511484f4ddb825824d0 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:29:50 +1200 Subject: [PATCH 463/722] New EasyConfig for zlib with the GCCcore 4.9.2 compiler --- .../z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..a7b3977bb9 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 74fa24f980d83f4c0bfed691b837d5137a807a0d Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:30:25 +1200 Subject: [PATCH 464/722] New EasyConfig for the GCC core -- GCC 4.9.2 compiler --- .../easyconfigs/g/GCCcore/GCCcore-4.9.2.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb new file mode 100644 index 0000000000..01f4776c64 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb @@ -0,0 +1,48 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '4.9.2' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.2' +gcc_name = 'GCC' + +source_urls = [ + 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + '%s-%s.tar.bz2' % (gcc_name.lower(), version), + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('binutils', '2.25'), +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' -- GitLab From 1d9edaed048b05f78f4c52c6c7e8b8985cd9dcd5 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:36:06 +1200 Subject: [PATCH 465/722] New EasyConfig for flex 2.5.39 with the GCCcore 4.9.2 toolchain --- .../f/flex/flex-2.5.39-GCCcore-4.9.2.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..71675a8b5c --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb @@ -0,0 +1,19 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.25', '', True) +] + +moduleclass = 'lang' -- GitLab From f0a867d2f56b99b4233ad60709796e966a1d9db7 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:40:26 +1200 Subject: [PATCH 466/722] New EasyConfig for M4 1.4.17 with the GCCcore 4.9.2 toolchain --- .../m/M4/M4-1.4.17-GCCcore-4.9.2.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..5551b81d85 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 6b51bde2d6ac315665b0bfe4c83df85a81bbd617 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 15:29:53 +1200 Subject: [PATCH 467/722] New EasyConfig for Bison 3.0.4 with the GCCcore 4.9.2 toolchain --- .../b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..159751eac5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From f055ab3a57d7eea9846742e9507bfc302ec8db05 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 15:39:05 +1200 Subject: [PATCH 468/722] New EasyConfig for numactl 2.0.11 with the GCCcore toolchain --- .../n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..49ba8f9bf3 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +builddependencies = [('binutils', '2.25')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' -- GitLab From d5737cc4992c7571f25173d5cabd1b68e76560d5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 18 Apr 2016 15:20:26 +0800 Subject: [PATCH 469/722] initial commit for BerkeleyGW-1.0.6 using intel-2016.02-GCC-4.9 toolchain (not working) --- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..6b0669dd87 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'BerkeleyGW' +version = "1.0.6" + +homepage = 'http://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk + periodic crystals to nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] +sources = ['BGW-%(version)s.tar.gz'] +checksums = ['8740562da41e87a62eb8d457675e4bfd'] + +files_to_copy = ['*'] + +prebuildopts = 'touch arch.mk; ' + +buildopts = 'all-flavors' + +parallel = 1 -- GitLab From 39fe8799dc0bf5b5332674dc40ea04a4b452d54c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 10:02:22 +0200 Subject: [PATCH 470/722] Bonnie++ with foss 2016a --- .../b/Bonnie++/Bonnie++-1.97-foss-2016a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb new file mode 100644 index 0000000000..4d9f9e29d3 --- /dev/null +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'Bonnie++' +version = '1.97' + +homepage = 'http://www.coker.com.au/bonnie++/' +description = """Bonnie++-1.97: Enhanced performance Test of Filesystem I/O""" + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://www.coker.com.au/bonnie++/experimental'] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['sbin/bonnie++'], + 'dirs': [] +} + +moduleclass = 'tools' + -- GitLab From b1c9ec39190cbd12d599b1f0df233e09bb29d230 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 10:25:51 +0200 Subject: [PATCH 471/722] remove DB eb file --- .../easyconfigs/d/DB/DB-4.8.30-foss2016a.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb deleted file mode 100644 index 0db26d6d7e..0000000000 --- a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'DB' -version = '4.8.30' - -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' -description = """Berkeley DB enables the development of custom data management solutions, - without the overhead traditionally associated with such custom projects.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['http://download.oracle.com/berkeley-db/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], - 'dirs': ['bin'], -} - -moduleclass = 'tools' -- GitLab From 23b49aa5020cb896337ae7875a886c2d51b0456d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 10:27:59 +0200 Subject: [PATCH 472/722] removed DB eb file --- .../easyconfigs/d/DB/DB-4.8.30-foss2016a.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb deleted file mode 100644 index 0db26d6d7e..0000000000 --- a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'DB' -version = '4.8.30' - -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' -description = """Berkeley DB enables the development of custom data management solutions, - without the overhead traditionally associated with such custom projects.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['http://download.oracle.com/berkeley-db/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], - 'dirs': ['bin'], -} - -moduleclass = 'tools' -- GitLab From 9a01d8b691c5da8fdda8188a18eb4a83458bb119 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 11:23:40 +0200 Subject: [PATCH 473/722] export path --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index efd22bd922..19d6de4aa0 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -3,7 +3,6 @@ easyblock = 'PerlModule' name = 'DB_File' version = '1.835' versionsuffix = '-Perl-%(perlver)s' -preinstallopts = 'export DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib' @@ -20,6 +19,8 @@ dependencies = [ ('DB', '6.2.23'), ] +preinstallopts = 'export DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" && ' + sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], -- GitLab From 29a97dd8e9370b38c0947ec500a17f4ef87b2997 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 18 Apr 2016 17:24:34 +0800 Subject: [PATCH 474/722] initial support of Wannier90-1.2 and 2.0.1 with intel-2016.02-GCC-4.9 --- .../Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 25 ++++++++++++++++++ .../Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 26 +++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..71d744077f --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '1.2' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] + +# ugly hack +prebuildopts = 'rm make.sys; touch make.sys; ' +prebuildopts += 'F90=ifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' + +files_to_copy = [(['wannier90.x'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..e7a229fa5e --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '2.0.1' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] + +# ugly hack +prebuildopts = 'rm make.sys; touch make.sys; ' +prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x'], + 'dirs': [] +} + +moduleclass = 'chem' -- GitLab From 6e96e854e1786abe3f0676ea977c038f95fe4f5f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 12:58:45 +0200 Subject: [PATCH 475/722] export path --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 19d6de4aa0..b03011fb99 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -4,8 +4,6 @@ name = 'DB_File' version = '1.835' versionsuffix = '-Perl-%(perlver)s' - - homepage = 'http://perldoc.perl.org/DB_File.html' description = """Perl5 access to Berkeley DB version 1.x.""" @@ -19,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preinstallopts = 'export DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" && ' +preinstallopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], @@ -27,3 +25,4 @@ sanity_check_paths = { } moduleclass = 'data' + -- GitLab From 8a14112aef54d4ff60bfdc915e2ef1c573862fe4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 13:15:33 +0200 Subject: [PATCH 476/722] preconfigopts --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index b03011fb99..85e0ba3145 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preinstallopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' +preconfigopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], -- GitLab From e54a2cf119497b7be7322575ab5e5d7bc7efb450 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 13:17:23 +0200 Subject: [PATCH 477/722] brackets --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 85e0ba3145..326da3c949 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preconfigopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' +preconfigopts = 'DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], -- GitLab From 281ca1e55eba6725c38c3908d3a9f79d7c294769 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 18 Apr 2016 13:45:40 +0200 Subject: [PATCH 478/722] Add easyconfigs for SIONlib (regular and tools) --- .../SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb | 41 +++++++++++++++++++ .../s/SIONlib/SIONlib-1.6.1-foss-2016a.eb | 37 +++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb new file mode 100644 index 0000000000..b8509256ef --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.6.1' +versionsuffix = '-tools' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. This package provides a stripped-down + installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against a tool requiring + a different SIONlib version.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['sionlib-%(version)sl.tar.gz'] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)sl'] + +checksums = [ + '57208e08309cf8892fe3daee90567d21', # sionlib-1.6.1l.tar.gz +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb new file mode 100644 index 0000000000..a093e042cb --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb @@ -0,0 +1,37 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.6.1' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. SIONlib provides different interfaces: + parallel access using MPI, OpenMP, or their combination, and sequential access for post-processing + utilities.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)s'] + +checksums = [ + '47113ebc00ae38c4f0965659427a0242', # sionlib-1.6.1.tar.gz +] + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['sioncom', 'siongen', 'sionser']], + 'dirs': [] +} + +moduleclass = 'lib' -- GitLab From aaee1240312cea617f9b801a5f04aaaa4c0cb7e4 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 18 Apr 2016 15:27:53 +0200 Subject: [PATCH 479/722] As requested, comment on the tools version --- .../easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb index b8509256ef..e773779617 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb @@ -10,6 +10,8 @@ easyblock = 'ConfigureMake' name = 'SIONlib' version = '1.6.1' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details versionsuffix = '-tools' homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' -- GitLab From 9cca4fb7a7bde5cc26ae1676c8bae8ef71ca0b3f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 18 Apr 2016 13:33:17 -0400 Subject: [PATCH 480/722] add IPython 3.2.3 easyconfig for foss 2016a toolchain --- .../IPython-3.2.3-foss-2016a-Python-2.7.11.eb | 85 +++++++++++++++++++ .../l/libsodium/libsodium-1.0.8-foss-2016a.eb | 20 +++++ .../o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb | 27 ++++++ ...MQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb | 29 +++++++ .../util-linux-2.27.1-foss-2016a.eb | 33 +++++++ .../z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb | 35 ++++++++ 6 files changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..02467990c5 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,85 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..ef8bb83cbf --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.8' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb new file mode 100644 index 0000000000..5f92dedd69 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb new file mode 100644 index 0000000000..c279b32410 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.2.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +dependencies = [ + ('Python', '2.7.11'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb new file mode 100644 index 0000000000..6e398ddd1e --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.27.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb new file mode 100644 index 0000000000..c67d70fb3a --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.1.4' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.27.1'), + ('libsodium', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 832b44908ab598ddc706fcd9b75c51e5f3d9103f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 18 Apr 2016 17:04:21 -0400 Subject: [PATCH 481/722] add Eigen 3.2.7 for foss 2016a --- .../easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb new file mode 100644 index 0000000000..a45d43c1fa --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.7' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From 2695a9a0755c6dc34e0df8aa241c928479718f44 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 18 Apr 2016 17:53:55 -0400 Subject: [PATCH 482/722] include MarkupSafe 0.23 in exts_list --- .../i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb index 02467990c5..f70668f24c 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -48,6 +48,9 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), -- GitLab From 0586ff6d4fcacfd2c8d8b8135c9837d5e2fce4f2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 07:04:59 +0800 Subject: [PATCH 483/722] fix prebuildopts --- .../w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 2 +- .../w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index 71d744077f..5359496146 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' +prebuildopts += 'F90=ifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x'], 'bin')] diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index e7a229fa5e..631f9e28bc 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -14,7 +14,8 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' +prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] -- GitLab From b5def49e41686976750ad72b309f87a423364a69 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 19 Apr 2016 13:45:29 +1200 Subject: [PATCH 484/722] Removed binutils-2.26 as it is untested and unneeded --- .../b/binutils/binutils-2.26-GCCcore-4.9.2.eb | 42 ------------------- 1 file changed, 42 deletions(-) delete mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb deleted file mode 100644 index 75c194bc7b..0000000000 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'binutils' -version = '2.26' - -homepage = 'http://directory.fsf.org/project/binutils/' -description = "binutils: GNU binary utilities" - -toolchain = {'name': 'GCCcore', 'version': '4.9.2'} - -sources = [SOURCE_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [ - ('M4', '1.4.17'), - ('flex', '2.6.0'), - ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep - ('zlib', '1.2.8'), - # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) -] - -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - -moduleclass = 'tools' -- GitLab From 51f553d9979e251dbf093b75ca12bb52fa5006c3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 15:16:10 +0800 Subject: [PATCH 485/722] replace hardcoded ifort with $F90 --- .../w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 2 +- .../w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index 5359496146..73eeb08ff4 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +prebuildopts += 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x'], 'bin')] diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index 631f9e28bc..e4b353566b 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +prebuildopts += 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] -- GitLab From 5ee511dc03e1383691dcf9ce3ce7740a5b091115 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 15:39:45 +0800 Subject: [PATCH 486/722] also build and install library --- .../w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 7 +++++-- .../w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 7 +++++-- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index 73eeb08ff4..a1e273882c 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -15,10 +15,13 @@ source_urls = ['http://www.wannier.org/code'] prebuildopts = 'rm make.sys; touch make.sys; ' prebuildopts += 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' -files_to_copy = [(['wannier90.x'], 'bin')] +# build program and library +buildopts = 'all' + +files_to_copy = [(['wannier90.x'], 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x'], + 'files': ['bin/wannier90.x', 'lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index e4b353566b..c85a2e8e7c 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -17,10 +17,13 @@ prebuildopts = 'rm make.sys; touch make.sys; ' prebuildopts += 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] +# build program and library +buildopts = "all" + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x'], + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], 'dirs': [] } -- GitLab From 0332209ac50434cc5c4839baf8e2b627403ba653 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 15:53:41 +0800 Subject: [PATCH 487/722] replace ugly hack with patch --- .../Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 6 +++--- .../Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 6 +++--- .../w/Wannier90/Wannier90_1x_ignore_makesys.patch | 11 +++++++++++ .../w/Wannier90/Wannier90_2x_ignore_makesys.patch | 11 +++++++++++ 4 files changed, 28 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index a1e273882c..e92974ac88 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.wannier.org/code'] -# ugly hack -prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +patches = ['Wannier90_1x_ignore_makesys.patch'] + +prebuildopts = 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' # build program and library buildopts = 'all' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index c85a2e8e7c..acef4f4eb1 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -12,9 +12,9 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.wannier.org/code'] -# ugly hack -prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +patches = ['Wannier90_2x_ignore_makesys.patch'] + +prebuildopts = 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' # build program and library diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch new file mode 100644 index 0000000000..66cb495806 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch @@ -0,0 +1,11 @@ +--- src/Makefile.orig 2016-04-19 15:26:27.373047000 +0800 ++++ src/Makefile 2016-04-19 15:26:32.414229150 +0800 +@@ -1,7 +1,7 @@ + # Should be no need to change below this line + # + +-include ../make.sys ++#include ../make.sys + + OBJS = constants.o io.o utility.o parameters.o hamiltonian.o overlap.o \ + kmesh.o disentangle.o wannierise.o plot.o transport.o diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch new file mode 100644 index 0000000000..fa4a6de14a --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch @@ -0,0 +1,11 @@ +--- src/Makefile.2.orig 2016-04-19 15:29:17.248672000 +0800 ++++ src/Makefile.2 2016-04-19 15:29:21.648448096 +0800 +@@ -1,7 +1,7 @@ + # Should be no need to change below this line + # + +-include ../../make.sys ++#include ../../make.sys + + OBJS = constants.o io.o utility.o parameters.o hamiltonian.o overlap.o \ + kmesh.o disentangle.o wannierise.o plot.o transport.o -- GitLab From 449cc75fd5e13863595ea0e308c1b36c3d644962 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 17:52:05 +0800 Subject: [PATCH 488/722] add explanatory comments to patch files --- .../easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch | 2 ++ .../easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch index 66cb495806..07fb605587 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch @@ -1,3 +1,5 @@ +avoid including make.sys, which contains hardcoding settings we don't need/want +author: Miguel Dias Costa (National University of Singapore) --- src/Makefile.orig 2016-04-19 15:26:27.373047000 +0800 +++ src/Makefile 2016-04-19 15:26:32.414229150 +0800 @@ -1,7 +1,7 @@ diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch index fa4a6de14a..8bf5e9aa01 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch @@ -1,3 +1,5 @@ +avoid including make.sys, which contains hardcoding settings we don't need/want +author: Miguel Dias Costa (National University of Singapore) --- src/Makefile.2.orig 2016-04-19 15:29:17.248672000 +0800 +++ src/Makefile.2 2016-04-19 15:29:21.648448096 +0800 @@ -1,7 +1,7 @@ -- GitLab From 777c8581b0c4d9f63871586b1a28ff6d0f39fc61 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 19 Apr 2016 14:21:08 +0200 Subject: [PATCH 489/722] removed newline --- easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb index 4d9f9e29d3..f63a76fa69 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb @@ -26,4 +26,3 @@ sanity_check_paths = { } moduleclass = 'tools' - -- GitLab From 5ae36bfe05d535e1d664cd00d5bb0747a4eb051d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 19 Apr 2016 14:22:53 +0200 Subject: [PATCH 490/722] use of env --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 326da3c949..8c069fec94 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preconfigopts = 'DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], -- GitLab From 7010b4032c4c42ea200bdcc329aa738a607c5863 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 15:04:01 +0200 Subject: [PATCH 491/722] add easyconfig LLVM-3.8.0-intel-2016a.eb, add easyconfig CMake-3.5.2-intel-2016a.eb --- .../c/CMake/CMake-3.5.2-intel-2016a.eb | 31 +++++++++++++++ .../l/LLVM/LLVM-3.8.0-intel-2016a.eb | 39 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb new file mode 100644 index 0000000000..6d07f31ebd --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb new file mode 100644 index 0000000000..1aa8a611cd --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.5.1'), + ('Python', '2.7.11'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' -- GitLab From 2f12335cd3d739900ac625cc64cee51876236104 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 15:08:40 +0200 Subject: [PATCH 492/722] modify easyconfig LLVM-3.8.0-intel-2016a.eb --- easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb index 1aa8a611cd..7a9543d260 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb @@ -28,9 +28,11 @@ dependencies = [ ] configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON" sanity_check_paths = { - 'files': ['bin/llvm-ar'], + 'files': ['bin/llvm-ar', 'bin/FileCheck'], 'dirs': ['include/llvm', 'include/llvm-c'], } -- GitLab From f8842a7e96418b884e6dbdbfa0eb6d8f59dc7981 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 20:12:42 +0200 Subject: [PATCH 493/722] add easyconfig Rust-1.8.0-intel-2016a.eb --- .../r/Rust/Rust-1.8.0-intel-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb new file mode 100644 index 0000000000..e2f00427e8 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.8.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] + +builddependencies = [('Python', '2.7.11')] + +dependencies = [ + ('LLVM', '3.8.0'), +] + +configopts = "--llvm-root=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' -- GitLab From eaef4d4ce138181088a256bc62175b61bda94114 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 22:05:31 +0200 Subject: [PATCH 494/722] add easyconfig HDF-4.2.11-intel-2016a.eb --- .../h/HDF/HDF-4.2.11-intel-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb new file mode 100644 index 0000000000..1d7ce9b8e5 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.11' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] +dependencies = [ + ('Szip', '2.1'), +] + +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' -- GitLab From b0b683b2d704da4733dd791e2041277c6be48968 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Tue, 19 Apr 2016 23:31:46 -0400 Subject: [PATCH 495/722] add libQGLViewer easyconfig for foss 2016a --- .../libQGLViewer-2.6.3-foss-2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb new file mode 100644 index 0000000000..12e821c14c --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'EB_libQGLViewer' + +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Qt', '4.8.7')] + +start_dir = '%(builddir)s/libQGLViewer-2.6.3/QGLViewer' + +moduleclass = 'lib' -- GitLab From 2a6a0dcb8c30c4edc6ac385c528b424601686ee1 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 20 Apr 2016 01:15:13 -0400 Subject: [PATCH 496/722] add GDB 7.10.1 easyconfig for foss 2016a --- .../GDB-7.10.1-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..7a28658458 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('Python', '2.7.11'), +] + +configopts = '--with-python' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' -- GitLab From e331243065a34afc93b9af7cc0603fc8faff5b89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Apr 2016 09:30:40 +0200 Subject: [PATCH 497/722] modify easyconfig HDF-4.2.11-intel-2016a.eb --- easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb index 1d7ce9b8e5..28e5e6ad36 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ ('Szip', '2.1'), + ('libjpeg-turbo', '1.4.2'), ] configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" -- GitLab From 62cc9b3e75ad621c2b74b36f8d6afe3c373c39d9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:16:16 +0200 Subject: [PATCH 498/722] Adjusted MADlib to supported postgresql version --- .../MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb index 35ae5d23c5..074b5142d7 100644 --- a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb @@ -12,18 +12,25 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = ['apache-madlib-%(version)s-incubating-source.tar.gz'] source_urls = ['https://dist.apache.org/repos/dist/release/incubator/madlib/%(version)s-incubating'] -builddependencies = [('CMake', '3.4.3')] +builddependencies = [ + ('CMake', '3.4.3'), + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('M4', '1.4.17'), + ('Boost', '1.60.0', versionsuffix), + ('Eigen', '3.2.7'), + ('PyXB', '1.2.4', versionsuffix), +] dependencies = [ ('Python', '2.7.11'), - ('PostgreSQL', '9.5.2', versionsuffix), + ('PostgreSQL', '9.4.7', versionsuffix), ] separate_build_dir = True sanity_check_paths = { 'files': ['bin/madpack'], - 'dirs': [] } moduleclass = 'data' -- GitLab From 5ad7cefb45a8dc6d5129d7196242ccd18fd01f2c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:47:49 +0200 Subject: [PATCH 499/722] Add Postgres-XL --- ...gres-XL-9.5r1-intel-2016a-Python-2.7.11.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..01c5da8a48 --- /dev/null +++ b/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Postgres-XL' +version = '9.5r1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.postgres-xl.org' +description = """Postgres-XL is a horizontally scalable open source SQL database cluster, +flexible enough to handle varying database workloads:""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://files.postgres-xl.org'] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.22.1'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' -- GitLab From ef50f1d4407173b2965c5a94a07d89f9a83fdb40 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:48:32 +0200 Subject: [PATCH 500/722] Add PostgreSQL 9.4.7 (needed for compatibility of MADlib) --- ...tgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..20f36a2447 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.4.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.mysql.com/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.22.1'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From fa95df64e5dc0ca93d6df41a3c32f7d125be6d22 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:52:01 +0200 Subject: [PATCH 501/722] Drop MADlib in this PR --- .../MADlib-1.9-intel-2016a-Python-2.7.11.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb deleted file mode 100644 index 074b5142d7..0000000000 --- a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'MADlib' -version = '1.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://madlib.incubator.apache.org' -description = """MADlib: Big Data Machine Learning in SQL for Data Scientists""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = ['apache-madlib-%(version)s-incubating-source.tar.gz'] -source_urls = ['https://dist.apache.org/repos/dist/release/incubator/madlib/%(version)s-incubating'] - -builddependencies = [ - ('CMake', '3.4.3'), - ('Bison', '3.0.4'), - ('flex', '2.6.0'), - ('M4', '1.4.17'), - ('Boost', '1.60.0', versionsuffix), - ('Eigen', '3.2.7'), - ('PyXB', '1.2.4', versionsuffix), -] - -dependencies = [ - ('Python', '2.7.11'), - ('PostgreSQL', '9.4.7', versionsuffix), -] - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['bin/madpack'], -} - -moduleclass = 'data' -- GitLab From 677926d3c95857f05067e4b2c6fc06088948ef07 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 11:02:33 +0200 Subject: [PATCH 502/722] Extend sanity check postgreSQL --- .../PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 4 ++-- .../PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb index 20f36a2447..9afa456cae 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -37,8 +37,8 @@ builddependencies = [ configopts = '--with-python --with-openssl' sanity_check_paths = { - 'files': ['bin/psql'], - 'dirs': [], + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index a7590c6580..fca7dea11c 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -37,8 +37,8 @@ builddependencies = [ configopts = '--with-python --with-openssl' sanity_check_paths = { - 'files': ['bin/psql'], - 'dirs': [], + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], } moduleclass = 'data' -- GitLab From 40dfcc220736688ada38def26b300fd15ae280ed Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 17:46:24 +0800 Subject: [PATCH 503/722] use patch to disable including arck.mk and define everything in prebuildopts --- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 19 +++++++--- ...keleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 35 +++++++++++++++++++ .../BerkeleyGW/BerkeleyGW_ignore_archmk.patch | 12 +++++++ 3 files changed, 62 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 6b0669dd87..7b6ed07c7d 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -4,8 +4,8 @@ name = 'BerkeleyGW' version = "1.0.6" homepage = 'http://www.berkeleygw.org' -description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle - properties and the optical responses of a large variety of materials from bulk +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} @@ -15,10 +15,21 @@ source_urls = ['http://www.berkeleygw.org/releases/'] sources = ['BGW-%(version)s.tar.gz'] checksums = ['8740562da41e87a62eb8d457675e4bfd'] +patches = ['BerkeleyGW_ignore_archmk.patch'] + files_to_copy = ['*'] -prebuildopts = 'touch arch.mk; ' +prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' +prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' +prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' +prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' buildopts = 'all-flavors' -parallel = 1 +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..2001776308 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'BerkeleyGW' +version = "1.1-beta2" + +homepage = 'http://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk + periodic crystals to nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] +sources = ['BGW-%(version)s.tar.gz'] +checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] + +patches = ['BerkeleyGW_ignore_archmk.patch'] + +files_to_copy = ['*'] + +prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' +prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' +prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' +prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' + +buildopts = 'all-flavors' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch new file mode 100644 index 0000000000..47898699a6 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch @@ -0,0 +1,12 @@ +avoid including arch.mk, which contains hardcoding settings we don't need/want +author: Miguel Dias Costa (National University of Singapore) +--- Common/common-rules.mk.orig 2016-04-20 13:44:00.254262000 +0800 ++++ Common/common-rules.mk 2016-04-20 13:44:07.830742486 +0800 +@@ -1,5 +1,5 @@ +-$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) +-include $(PREFIX)/arch.mk ++#$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) ++#include $(PREFIX)/arch.mk + + ifneq ($(wildcard $(PREFIX)/flavor.mk),) + include $(PREFIX)/flavor.mk -- GitLab From cb89189505ade779e2cd9cb9da9bb29f254db6fc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 13:23:46 +0200 Subject: [PATCH 504/722] ALPS now builds! --- .../ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb | 8 ++++---- .../a/ALPS/ALPS-2.2.b4-python-embedding.patch | 14 ++++++++++++++ 2 files changed, 18 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb index cf98c0aae4..ce0520f4ab 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://alps.comp-phys.org/static/software/releases'] +patches = ['ALPS-%(version)s-python-embedding.patch'] + builddependencies = [('CMake', '3.4.3')] dependencies = [ @@ -29,11 +31,9 @@ configopts += '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' separate_build_dir = True -maxparallel = 1 - sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['bin/alpspython', 'lib/libalps.%s' % SHLIB_EXT], + 'dirs': ['include/alps', 'lib/python'] } moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch new file mode 100644 index 0000000000..5927e2e784 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch @@ -0,0 +1,14 @@ +# To embed python, it must return a list of needed libraries with `;` instead of whitespace +# Ward Poelmans +diff -ur alps-2.2.b4-src.orig/alps/config/FindPython.cmake alps-2.2.b4-src/alps/config/FindPython.cmake +--- alps-2.2.b4-src.orig/alps/config/FindPython.cmake 2015-09-20 21:21:42.000000000 +0200 ++++ alps-2.2.b4-src/alps/config/FindPython.cmake 2016-04-20 11:28:18.828407677 +0200 +@@ -160,7 +160,7 @@ + # + # libraries which must be linked in when embedding + # +- EXEC_PYTHON_SCRIPT ("from distutils.sysconfig import * ;print (str(get_config_var('LOCALMODLIBS')) + ' ' + str(get_config_var('LIBS'))).strip()" ++ EXEC_PYTHON_SCRIPT ("from distutils.sysconfig import * ;print (str(get_config_var('LOCALMODLIBS')) + ' ' + str(get_config_var('LIBS'))).strip().replace(' ', ';')" + PYTHON_EXTRA_LIBS) + MESSAGE(STATUS "PYTHON_EXTRA_LIBS =${PYTHON_EXTRA_LIBS}" ) + mark_as_advanced(PYTHON_EXTRA_LIBS) -- GitLab From 523b4f05f0dc5b78abb1323e9ddf4cdbab5a86ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Apr 2016 13:26:34 +0200 Subject: [PATCH 505/722] add easyconfig Rust-1.8.0-foss-2016a.eb --- .../r/Rust/Rust-1.8.0-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb new file mode 100644 index 0000000000..2254e51fbf --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.8.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] + +builddependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' -- GitLab From 240bbc87f7f4d346cedc3b29e326d7103fc24898 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 13:35:52 +0200 Subject: [PATCH 506/722] Let ALPS find Szip --- .../a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb index ce0520f4ab..74ee42be3a 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb @@ -20,14 +20,14 @@ builddependencies = [('CMake', '3.4.3')] dependencies = [ ('zlib', '1.2.8'), + ('Szip', '2.1'), ('Python', '2.7.11'), ('Boost', '1.58.0', versionsuffix), ('HDF5', '1.8.16'), ('matplotlib', '1.5.1', versionsuffix), ] -configopts = '-DSZIP_INCLUDE_DIR=$EBROOTSZIP/include -DSZIP_LIBRARY=$EBROOTSZIP/lib ' -configopts += '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' +configopts = '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' separate_build_dir = True -- GitLab From 11b5379ba4bf016e2b2346f903746b7fd7f76a2f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 13:52:50 +0200 Subject: [PATCH 507/722] Fix remarks --- ...ntel-2016a.eb => GDB-7.11-intel-2016a-Python-2.7.11.eb} | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/GDB/{GDB-7.11-intel-2016a.eb => GDB-7.11-intel-2016a-Python-2.7.11.eb} (95%) diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb similarity index 95% rename from easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb rename to easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb index fa5295e98e..7f2305c130 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb @@ -2,14 +2,17 @@ easyblock = 'ConfigureMake' name = 'GDB' version = '7.11' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "The GNU Project Debugger" +toolchain = {'name': 'intel', 'version': '2016a'} + sources = [SOURCELOWER_TAR_XZ] source_urls = [GNU_SOURCE] -toolchain = {'name': 'intel', 'version': '2016a'} +patches = ['GDB-7.9-missing-makeinfo.patch'] dependencies = [ ('zlib', '1.2.8'), @@ -19,8 +22,6 @@ dependencies = [ ('Python', '2.7.11'), ] -patches = ['GDB-7.9-missing-makeinfo.patch'] - configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' configopts += '--with-system-readline --enable-tui --enable-plugins' -- GitLab From 2f64f6c34e127ecd2095843c44409d7690926f31 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 14:52:09 +0200 Subject: [PATCH 508/722] Add explicit include for fslsurface --- easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb index 145ff09b91..a26ad87936 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb @@ -14,6 +14,8 @@ patches = [ 'FSL_icc_nan-inf_fix.patch', ] +preconfigopts = 'CFLAGS="-I%(builddir)s/src $CFLAGS"' + dependencies = [ ('freeglut', '3.0.0'), ('expat', '2.1.0'), -- GitLab From 3993ccc5f2970b1a36159c23a3681e14c025a912 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 15:00:08 +0200 Subject: [PATCH 509/722] Fix Werror error for MariaDB --- .../m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 8 ++++++-- .../m/MariaDB/MariaDB-10.1.13-remove-Werror.patch | 14 ++++++++++++++ 2 files changed, 20 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index 68f736cb1a..9a05f86ff3 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -11,19 +11,23 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-%(version)s-remove-Werror.patch'] + dependencies = [ ('zlib', '1.2.8'), ('ncurses', '6.0'), ('jemalloc', '4.1.0'), ('PCRE', '8.38'), ('XZ', '5.2.2'), - ('Boost', '1.60.0'), + ('Boost', '1.60.0', '-Python-2.7.11'), ('libxml2', '2.9.3'), ] builddependencies = [('CMake', '3.4.3')] -configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DWITH_INNODB_LZMA=on" +separate_build_dir = True + +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DMYSQL_MAINTAINER_MODE=ON" sanity_check_paths = { 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch new file mode 100644 index 0000000000..c7d04caf71 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch @@ -0,0 +1,14 @@ +diff -ur mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake +--- mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-03-24 10:12:12.000000000 +0100 ++++ mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-04-20 14:29:31.019940551 +0200 +@@ -156,8 +156,8 @@ + endif () + + ## always want these +-set(CMAKE_C_FLAGS "-Wall -Werror ${CMAKE_C_FLAGS}") +-set(CMAKE_CXX_FLAGS "-Wall -Werror ${CMAKE_CXX_FLAGS}") ++set(CMAKE_C_FLAGS "-Wall ${CMAKE_C_FLAGS}") ++set(CMAKE_CXX_FLAGS "-Wall ${CMAKE_CXX_FLAGS}") + + ## need to set -stdlib=libc++ to get real c++11 support on darwin + if (APPLE) -- GitLab From 7cf6555d3c10191f880df6b26dc146d344d44093 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 15:03:08 +0200 Subject: [PATCH 510/722] Add doc in patch for Mariadb --- .../easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch index c7d04caf71..eb1812a0ff 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch @@ -1,3 +1,5 @@ +# This -Werror will cause the build to fail because of a warning about using the intel compiler +# Ward Poelmans diff -ur mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake --- mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-03-24 10:12:12.000000000 +0100 +++ mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-04-20 14:29:31.019940551 +0200 -- GitLab From 7329ac036396459a8d987ba66b18919854db545a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 21:51:03 +0800 Subject: [PATCH 511/722] use env --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 7b6ed07c7d..573492b3f2 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -19,7 +19,7 @@ patches = ['BerkeleyGW_ignore_archmk.patch'] files_to_copy = ['*'] -prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 2001776308..509645960b 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -19,7 +19,7 @@ patches = ['BerkeleyGW_ignore_archmk.patch'] files_to_copy = ['*'] -prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' -- GitLab From 730ffa4793fdb863db56e34ddd1624b256e014de Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 21:52:12 +0800 Subject: [PATCH 512/722] use short indent in description --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 4 ++-- .../BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 573492b3f2..cf8c1e41cf 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -5,8 +5,8 @@ version = "1.0.6" homepage = 'http://www.berkeleygw.org' description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle - properties and the optical responses of a large variety of materials from bulk - periodic crystals to nanostructures such as slabs, wires and molecules.""" + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 509645960b..2b7d7dc5ed 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -5,8 +5,8 @@ version = "1.1-beta2" homepage = 'http://www.berkeleygw.org' description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle - properties and the optical responses of a large variety of materials from bulk - periodic crystals to nanostructures such as slabs, wires and molecules.""" + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} -- GitLab From 57cea100f5dbffb25d4f5eab4e15303622ab55a7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 16:23:37 +0200 Subject: [PATCH 513/722] Mariadb: link to -lrt --- .../m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 5 ++++- .../MariaDB-10.1.13-link-rt-for-jemalloc.patch | 14 ++++++++++++++ 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index 9a05f86ff3..ae90e1a3ed 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] sources = [SOURCELOWER_TAR_GZ] -patches = ['MariaDB-%(version)s-remove-Werror.patch'] +patches = [ + 'MariaDB-%(version)s-remove-Werror.patch', + 'MariaDB-%(version)s-link-rt-for-jemalloc.patch', +] dependencies = [ ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch new file mode 100644 index 0000000000..780c41af5b --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch @@ -0,0 +1,14 @@ +# On older systems (like RHEL 6), jemalloc must also link to -lrt for getclock +# On RHEL 7 and greater, this is not needed as it's part of libc there. +# Ward Poelmans +diff -ur mariadb-10.1.13.orig/cmake/jemalloc.cmake mariadb-10.1.13/cmake/jemalloc.cmake +--- mariadb-10.1.13.orig/cmake/jemalloc.cmake 2016-03-24 10:12:10.000000000 +0100 ++++ mariadb-10.1.13/cmake/jemalloc.cmake 2016-04-20 16:21:18.102681504 +0200 +@@ -21,6 +21,7 @@ + SET(what bundled) + ELSE() + SET(libname jemalloc c) ++ SET(CMAKE_REQUIRED_LIBRARIES r) + SET(what system) + ENDIF() + -- GitLab From 6a3bab838e81554fef00f818ee20c01190c71f50 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 22:27:47 +0800 Subject: [PATCH 514/722] use ConfigureMake skipping configure instead of MakeCp --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 6 ++++-- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index cf8c1e41cf..570e1b3636 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'BerkeleyGW' version = "1.0.6" @@ -17,7 +17,7 @@ checksums = ['8740562da41e87a62eb8d457675e4bfd'] patches = ['BerkeleyGW_ignore_archmk.patch'] -files_to_copy = ['*'] +skipsteps = ['configure'] prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' @@ -27,6 +27,8 @@ prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLA buildopts = 'all-flavors' +installopts = 'INSTDIR=%(installdir)s' + sanity_check_paths = { 'files': [], 'dirs': ['bin'] diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 2b7d7dc5ed..4c7949cc07 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'BerkeleyGW' version = "1.1-beta2" @@ -17,7 +17,7 @@ checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] patches = ['BerkeleyGW_ignore_archmk.patch'] -files_to_copy = ['*'] +skipsteps = ['configure'] prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' @@ -27,6 +27,8 @@ prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLA buildopts = 'all-flavors' +installopts = 'INSTDIR=%(installdir)s' + sanity_check_paths = { 'files': [], 'dirs': ['bin'] -- GitLab From f3cb8d07b5b4c94abec4f892c8041313ee7f569f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 17:00:41 +0200 Subject: [PATCH 515/722] Typo fix --- .../m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch index 780c41af5b..c0a2cfee18 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch @@ -8,7 +8,7 @@ diff -ur mariadb-10.1.13.orig/cmake/jemalloc.cmake mariadb-10.1.13/cmake/jemallo SET(what bundled) ELSE() SET(libname jemalloc c) -+ SET(CMAKE_REQUIRED_LIBRARIES r) ++ SET(CMAKE_REQUIRED_LIBRARIES rt) SET(what system) ENDIF() -- GitLab From ee8043a440abb6accfb24a556ccdb1e391f8c3e9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 23:19:34 +0800 Subject: [PATCH 516/722] add most important binaries to sanity_check_path --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 6 ++++-- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 570e1b3636..2b338d6458 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,10 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': [], - 'dirs': ['bin'] + 'files': ['bin/'+name+'.'+flavor+'.x' + for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + for flavor in ['real', 'cplx']], + 'dirs': [] } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 4c7949cc07..42d4b94976 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,10 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': [], - 'dirs': ['bin'] + 'files': ['bin/'+name+'.'+flavor+'.x' + for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + for flavor in ['real', 'cplx']], + 'dirs': [] } moduleclass = 'chem' -- GitLab From 062b8f678410ec70835f69b578bf2778f8f4346a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 21 Apr 2016 00:04:37 +0800 Subject: [PATCH 517/722] don't redefine variable 'name' in sanity_check_path --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 4 ++-- .../BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 2b338d6458..452f967939 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,8 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+name+'.'+flavor+'.x' - for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + 'files': ['bin/'+prog+'.'+flavor+'.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] } diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 42d4b94976..04a46cfa50 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,8 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+name+'.'+flavor+'.x' - for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + 'files': ['bin/'+prog+'.'+flavor+'.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] } -- GitLab From 40d739240753148a555a9d0432149f88d93a293d Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 20 Apr 2016 16:47:30 -0400 Subject: [PATCH 518/722] including libGLU 9.0.0 as dependency --- .../l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb index 12e821c14c..cd9274f066 100644 --- a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb @@ -11,8 +11,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.libqglviewer.com/src/'] sources = [SOURCE_TAR_GZ] +dependencies = [ + ('libGLU', '9.0.0'), +] + builddependencies = [('Qt', '4.8.7')] -start_dir = '%(builddir)s/libQGLViewer-2.6.3/QGLViewer' +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' moduleclass = 'lib' -- GitLab From d85d97170461ddf8f1b654addca47fc8dfcd2897 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 21 Apr 2016 15:57:05 +0800 Subject: [PATCH 519/722] remove patch, copy generic arch.mk instead --- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 14 ++++++-------- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 14 ++++++-------- .../b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch | 12 ------------ 3 files changed, 12 insertions(+), 28 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 452f967939..ef88631251 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -15,17 +15,15 @@ source_urls = ['http://www.berkeleygw.org/releases/'] sources = ['BGW-%(version)s.tar.gz'] checksums = ['8740562da41e87a62eb8d457675e4bfd'] -patches = ['BerkeleyGW_ignore_archmk.patch'] - skipsteps = ['configure'] -prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' -prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' -prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' -prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' -prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' -buildopts = 'all-flavors' +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' +buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' installopts = 'INSTDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 04a46cfa50..07d5635dac 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -15,17 +15,15 @@ source_urls = ['http://www.berkeleygw.org/releases/'] sources = ['BGW-%(version)s.tar.gz'] checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] -patches = ['BerkeleyGW_ignore_archmk.patch'] - skipsteps = ['configure'] -prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' -prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' -prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' -prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' -prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' -buildopts = 'all-flavors' +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' +buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' installopts = 'INSTDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch deleted file mode 100644 index 47898699a6..0000000000 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch +++ /dev/null @@ -1,12 +0,0 @@ -avoid including arch.mk, which contains hardcoding settings we don't need/want -author: Miguel Dias Costa (National University of Singapore) ---- Common/common-rules.mk.orig 2016-04-20 13:44:00.254262000 +0800 -+++ Common/common-rules.mk 2016-04-20 13:44:07.830742486 +0800 -@@ -1,5 +1,5 @@ --$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) --include $(PREFIX)/arch.mk -+#$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) -+#include $(PREFIX)/arch.mk - - ifneq ($(wildcard $(PREFIX)/flavor.mk),) - include $(PREFIX)/flavor.mk -- GitLab From d62ec8db0c825e6d49318e8b7ca39ae771e67717 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 21 Apr 2016 15:58:49 +0800 Subject: [PATCH 520/722] edit homepage --- .../a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index ca4b5697db..a8183634de 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'ASE' version = '3.10.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://wiki.fysik.dtu.dk/ase/' +homepage = 'http://wiki.fysik.dtu.dk/ase' description = """ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.""" -- GitLab From 6c33d10734fc28919e332f46e9379110bcd0a316 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 21 Apr 2016 10:50:17 +0200 Subject: [PATCH 521/722] Fix remarks --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index e13485c431..7bee41cdcd 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -19,10 +19,10 @@ prebuildopts = "make dist && " sanity_check_paths = { 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, - 'lib/libjemalloc.so.2', 'include/jemalloc/jemalloc.h'], + 'include/jemalloc/jemalloc.h'], 'dirs': ['share'], } -modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.2']} +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} moduleclass = 'lib' -- GitLab From 6a4d11c588f7e31daf36f0f34262d769f3c1f92f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 08:41:23 +0800 Subject: [PATCH 522/722] generated with 'eb netCDF-Fortran-4.4.2-intel-2015b.eb --try-toolchain=intel,2016.02-GCC-4.9 -r' --- .../Bison-3.0.4-intel-2016.02-GCC-4.9.eb | 22 ++++++++++++ .../CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 31 +++++++++++++++++ .../cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb | 31 +++++++++++++++++ .../Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb | 19 +++++++++++ .../flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb | 14 ++++++++ ...DF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb | 26 ++++++++++++++ .../ncurses-5.9-intel-2016.02-GCC-4.9.eb | 18 ++++++++++ ...CDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb | 20 +++++++++++ .../netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb | 34 +++++++++++++++++++ .../s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb | 23 +++++++++++++ 10 files changed, 238 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..64d95d529f --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..c09f6ccec0 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..7135e0d493 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.45.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..6c27df0850 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.10' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.1'), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..154963c1c8 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..42dda90335 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.15-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..5385893f9b --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,18 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +# see https://bbs.archlinux.org/viewtopic.php?id=194029&p=3 +buildopts = 'CPP="$CC -E -P"' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..80d70623d7 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +version = '4.4.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.3.3.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..a58bf39670 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.3.3.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.15-patch1'), + ('cURL', '7.45.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.10'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..d8f05c9dd2 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From af63af4269d95dc953f708bbaf55655f30273915 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 15:17:53 +0800 Subject: [PATCH 523/722] [phys]{intel/2016.02-GCC-4.9} Yambo 3.4.2 --- .../Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..aaa16d016b --- /dev/null +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Yambo' +version = '3.4.2' + +homepage = 'http://www.yambo-code.org' +description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. + Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +dependencies = [('netCDF-Fortran', '4.4.2')] + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/yambo-3.4.2.tgz'] +checksums = ['f0820a0f42dfc81ce3811af647bed777'] + +configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' +configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' +configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff -L$EBROOTNETCDF/lib64 -lnetcdf"' + +buildopts = 'all' + +# no make install +buildininstalldir = 'True' +skipsteps = ['install'] +modextrapaths = {'PATH': '%(namelower)s-%(version)s/bin'} + +sanity_check_paths = { + 'files': ['%(namelower)s-%(version)s/bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', + 'yambo_kerr', 'yambo_ph', 'yambo_surf', 'ypp', 'ypp_ph', 'ypp_surf']], + 'dirs': [] +} + +moduleclass = 'phys' + +parallel = 1 -- GitLab From 2eca14f6b542eb457c27f4aebe36d6fb4496f7ee Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 15:30:48 +0800 Subject: [PATCH 524/722] bump ncurses to 6.0 --- .../easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb index c09f6ccec0..df5823de42 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' dependencies = [ - ('ncurses', '5.9'), + ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons #('OpenSSL', '1.0.1p'), -- GitLab From b76df745227c017890c908f28810ae55c805ae1b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 15:42:27 +0800 Subject: [PATCH 525/722] change module class --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index ef88631251..c0d639cc89 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -34,4 +34,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'chem' +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 07d5635dac..4700de27c4 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -34,4 +34,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'chem' +moduleclass = 'phys' -- GitLab From 22fc709acd211c30baf89829b9cafdaa0709e873 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 16:54:42 +0800 Subject: [PATCH 526/722] remove ncurses-5.9-intel-2016.02-GCC-4.9.eb --- .../ncurses-5.9-intel-2016.02-GCC-4.9.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb deleted file mode 100644 index 5385893f9b..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -# see https://bbs.archlinux.org/viewtopic.php?id=194029&p=3 -buildopts = 'CPP="$CC -E -P"' - -moduleclass = 'devel' -- GitLab From e20edb315e0af6f790c4efa27e69eb4f887bd960 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 17:29:16 +0800 Subject: [PATCH 527/722] bump HDF5 to 1.8.16 and cURL to 7.47.0 --- ...016.02-GCC-4.9.eb => cURL-7.47.0-intel-2016.02-GCC-4.9.eb} | 4 ++-- ...016.02-GCC-4.9.eb => HDF5-1.8.16-intel-2016.02-GCC-4.9.eb} | 2 +- .../n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/c/cURL/{cURL-7.45.0-intel-2016.02-GCC-4.9.eb => cURL-7.47.0-intel-2016.02-GCC-4.9.eb} (94%) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb => HDF5-1.8.16-intel-2016.02-GCC-4.9.eb} (96%) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb similarity index 94% rename from easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb rename to easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb index 7135e0d493..45e6650292 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'cURL' -version = '7.45.0' +version = '7.47.0' homepage = 'http://curl.haxx.se' description = """libcurl is a free and easy-to-use client-side URL transfer library, @@ -18,7 +18,7 @@ source_urls = ['http://curl.haxx.se/download/'] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -# dependencies = [('OpenSSL', '1.0.1p')] +# dependencies = [('OpenSSL', '1.0.1s')] # configopts = "--with-ssl=$EBROOTOPENSSL" modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb similarity index 96% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb index 42dda90335..d1c17ce30e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb @@ -1,5 +1,5 @@ name = 'HDF5' -version = '1.8.15-patch1' +version = '1.8.16' homepage = 'http://www.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb index a58bf39670..cff46757ad 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb @@ -16,8 +16,8 @@ source_urls = [ ] dependencies = [ - ('HDF5', '1.8.15-patch1'), - ('cURL', '7.45.0'), + ('HDF5', '1.8.16'), + ('cURL', '7.47.0'), ] builddependencies = [ -- GitLab From bc66427075d6045dce28ff41b2364668b5b56436 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 17:37:27 +0800 Subject: [PATCH 528/722] fix source_urls --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index aaa16d016b..f1e84f6a06 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ toolchainopts = {'usempi': True} dependencies = [('netCDF-Fortran', '4.4.2')] sources = [SOURCELOWER_TGZ] -source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/yambo-3.4.2.tgz'] +source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/'] checksums = ['f0820a0f42dfc81ce3811af647bed777'] configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' -- GitLab From 6eca75d940ee822d1eab2eb2c88e973f3b4d596a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 17:38:22 +0800 Subject: [PATCH 529/722] move dependencies below checksums --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index f1e84f6a06..bcb6f56739 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -10,12 +10,12 @@ description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid s toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} -dependencies = [('netCDF-Fortran', '4.4.2')] - sources = [SOURCELOWER_TGZ] source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/'] checksums = ['f0820a0f42dfc81ce3811af647bed777'] +dependencies = [('netCDF-Fortran', '4.4.2')] + configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' -- GitLab From 595721d4fb95078144d99129ff0a28a394b79ed2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 11:48:07 +0200 Subject: [PATCH 530/722] Biopython sanity check fix --- .../Biopython-1.65-foss-2016a-2.7.11.eb | 45 ------------------- ...Biopython-1.65-foss-2016a-Python-2.7.11.eb | 13 +++--- 2 files changed, 5 insertions(+), 53 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb deleted file mode 100644 index fc337c6c52..0000000000 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas -# License:: MIT/GPL -# -## -easyblock = "PythonPackage" - -name = 'Biopython' -version = '1.65' - -homepage = 'http://www.biopython.org' -description = """Biopython is a set of freely available tools for biological computation written -in Python by an international team of developers. It is a distributed collaborative effort to -develop Python libraries and applications which address the needs of current and future work in -bioinformatics. """ - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['http://biopython.org/DIST'] -sources = ['%(namelower)s-%(version)s.tar.gz'] - -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = "-%s-%s" % (python, pyver) - -dependencies = [ - (python, pyver), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, - 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ - pyshortver), - 'lib/python%s/site-packages/BioSQL' % pyshortver] -} - -options = {'modulename': 'Bio'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index 8730db898f..822334825f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -29,18 +29,15 @@ pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pyver), - ('numpy', '1.10.1', versionsuffix) + (python, pyver) ] sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, - 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ - pyshortver), - 'lib/python%s/site-packages/BioSQL' % pyshortver] + 'files': ['lib/python%(pyshortver)s/site-packages/biopython-%(version)s-py%(pyshortver)s.egg-info'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] } options = {'modulename': 'Bio'} -moduleclass = 'bio' +moduleclass = 'bio' \ No newline at end of file -- GitLab From 9bca295d623e5a844af78e774d8d2e8752b28006 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 11:49:20 +0200 Subject: [PATCH 531/722] String fix --- .../b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index 822334825f..f4b92dace0 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -26,7 +26,7 @@ python = 'Python' pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = "-%s-%s" % (python, pyver) +versionsuffix = "-%(python)s-%(pyver)s" dependencies = [ (python, pyver) -- GitLab From 5e94418f4931181e31c47d3be9882d0e6f232dc8 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 18:18:51 +0800 Subject: [PATCH 532/722] remove library paths, not needed --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index bcb6f56739..e98b1483ff 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -19,7 +19,7 @@ dependencies = [('netCDF-Fortran', '4.4.2')] configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' -configopts += '--with-netcdf-libs="-L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff -L$EBROOTNETCDF/lib64 -lnetcdf"' +configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' -- GitLab From 37731eef8b1705bc86ad2224890ed318bc6e4329 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 18:33:13 +0800 Subject: [PATCH 533/722] use $LIBFFT --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index e98b1483ff..4f192a0588 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -18,7 +18,7 @@ dependencies = [('netCDF-Fortran', '4.4.2')] configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' -configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' +configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="$LIBFFT" ' configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' -- GitLab From 98b99c783631409424f36993ac8b6a14de0f74ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 12:43:11 +0200 Subject: [PATCH 534/722] add easyconfig numexpr-2.5.2-intel-2016a-Python-2.7.11.eb --- ...numexpr-2.5.2-intel-2016a-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f3e0914bd5 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'numexpr' +version = '2.5.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From 4046ca8caf31526416dc2842edef61a8b2eb32b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 12:43:29 +0200 Subject: [PATCH 535/722] add easyconfig gdist-1.0.3-intel-2016a-Python-2.7.11.eb --- .../gdist-1.0.3-intel-2016a-Python-2.7.11.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f6f38f5d9f --- /dev/null +++ b/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'gdist' +version = '1.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/gdist' +description = """The gdist module is a Cython interface to a C++ library (http://code.google.com/p/geodesic/) for + computing geodesic distance which is the length of shortest line between two vertices on a triangulated mesh in three + dimensions, such that the line lies on the surface.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From 86b9fbf96e643400c35e6ce3eefa37323fe758a5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 12:43:44 +0200 Subject: [PATCH 536/722] ext list ? --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index c3ca739024..1e9c0c19f5 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -18,6 +18,12 @@ dependencies = [ ('DB_File', '1.835', versionsuffix), ] +exts_list = [ + ('CGI', '4.28', { + 'source_tmpl': 'CGI-4.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + }), +] options = {'modulename': 'Bio::Perl'} moduleclass = 'bio' -- GitLab From 5307a71e915dea2e5c22e0a634ffd5129298aac2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 12:43:52 +0200 Subject: [PATCH 537/722] add easyconfig NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb, add easyconfig PIL-1.1.7-intel-2016a-Python-2.7.11.eb, add easyconfig pydicom-0.9.9-intel-2016a-Python-2.7.11.eb --- ...NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb | 29 +++++++++++++++ .../PIL-1.1.7-intel-2016a-Python-2.7.11.eb | 36 +++++++++++++++++++ ...pydicom-0.9.9-intel-2016a-Python-2.7.11.eb | 26 ++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..77bcd52bff --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'NiBabel' +version = '2.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('PIL', '1.1.7', versionsuffix), + ('pydicom', '0.9.9', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f996585e10 --- /dev/null +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'PIL' +version = '1.1.7' +versionsuffix = '-Python-%(ppyver)s' + +homepage = 'http://www.pythonware.com/products/pil' +description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. + This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://effbot.org/downloads/'] +sources = ['Imaging-%(version)s.tar.gz'] + +patches = ['PIL-%(version)s-find-deps.patch'] + +pyver = '2.7.11' +versionsuffix = '-Python-%s' % pyver +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pyver), + ('libjpeg-turbo', '1.4.2'), + # currently not used because of dependency hell + # ('freetype', '2.6.1'), +] + +options = {'modulename': 'PIL'} + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%s/site-packages/%%(name)s' % pyshortver], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..ab11ff4c9f --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '0.9.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/darcymason/pydicom' +description = """Read, modify and write DICOM files with python code""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/darcymason/pydicom/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('Python', '2.7.11')] + +start_dir = 'source' + +options = {'modulename': 'dicom'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pydicom-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'data' -- GitLab From e2d71772432a501aed37e770db3eec9ea1ddcf08 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 18:58:14 +0800 Subject: [PATCH 538/722] switch to MakeCp with configure --- .../y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index 4f192a0588..23778bb6d6 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'Yambo' version = '3.4.2' @@ -16,6 +16,8 @@ checksums = ['f0820a0f42dfc81ce3811af647bed777'] dependencies = [('netCDF-Fortran', '4.4.2')] +with_configure = 'True' + configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="$LIBFFT" ' @@ -23,10 +25,7 @@ configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' -# no make install -buildininstalldir = 'True' -skipsteps = ['install'] -modextrapaths = {'PATH': '%(namelower)s-%(version)s/bin'} +files_to_copy = [(['bin/*'], 'bin')] sanity_check_paths = { 'files': ['%(namelower)s-%(version)s/bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', -- GitLab From d05d19be93bde3c4e31429ccaed73c50213b3406 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 13:43:38 +0200 Subject: [PATCH 539/722] modify easyconfig numexpr-2.5.2-intel-2016a-Python-2.7.11.eb --- .../n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb index f3e0914bd5..c352743328 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb @@ -11,7 +11,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'usempi': True} source_urls = ['https://github.com/pydata/numexpr/archive/'] sources = ['v%(version)s.tar.gz'] -- GitLab From 88ddd7a1b72945cb902ef2526ef8b8861b835be1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 13:51:17 +0200 Subject: [PATCH 540/722] modify easyconfig PIL-1.1.7-intel-2016a-Python-2.7.11.eb --- .../easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb index f996585e10..dabb8b2f35 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb @@ -27,10 +27,9 @@ dependencies = [ options = {'modulename': 'PIL'} -pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], - 'dirs': ['bin', 'lib/python%s/site-packages/%%(name)s' % pyshortver], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], } moduleclass = 'vis' -- GitLab From 47f5dbe7cec4797ad7745b808c06525bbb6c5c14 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 19:55:50 +0800 Subject: [PATCH 541/722] fix path in sanity checks --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index 23778bb6d6..d06eb6d47f 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -28,7 +28,7 @@ buildopts = 'all' files_to_copy = [(['bin/*'], 'bin')] sanity_check_paths = { - 'files': ['%(namelower)s-%(version)s/bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', + 'files': ['bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', 'yambo_kerr', 'yambo_ph', 'yambo_surf', 'ypp', 'ypp_ph', 'ypp_surf']], 'dirs': [] } -- GitLab From aa313b0431ca16e479e1be7c4795aa7befe6ad18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 14:34:28 +0200 Subject: [PATCH 542/722] usempi is not required for numexpr --- .../n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb | 1 - .../n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 1 - .../n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb | 1 - .../n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb index b59dd7b4f3..12e8271d88 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'usempi': True} source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 0f25285835..986566870c 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'usempi': True} source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb index 585a1680b7..7b2e107b82 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'usempi': True} source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb index a1e1df7d77..0012640a1c 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'usempi': True} source_urls = ['https://github.com/pydata/numexpr/archive/'] sources = ['v%(version)s.tar.gz'] -- GitLab From fbb287eb014e34d2f02e1f96ed017af399d46e51 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 14:44:11 +0200 Subject: [PATCH 543/722] add easyconfig PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb --- ...PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb new file mode 100644 index 0000000000..93ba3d3868 --- /dev/null +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'PIL' +version = '1.1.7' +versionsuffix = '-Python-%(ppyver)s' + +homepage = 'http://www.pythonware.com/products/pil' +description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. + This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://effbot.org/downloads/'] +sources = ['Imaging-%(version)s.tar.gz'] + +patches = ['PIL-%(version)s-find-deps.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + ('libjpeg-turbo', '1.4.2'), + ('freetype', '2.6.3'), +] + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' -- GitLab From e2ced009d6dec638e457588563d90907b8a2f26f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 14:52:58 +0200 Subject: [PATCH 544/722] Commet with foss2016a --- ...ommet-20160422-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..037900565c --- /dev/null +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'Commet' +version = '20160422' + +homepage = 'https://colibread.inria.fr/software/commet/' +description = """ COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# there is no tarball provided, only git checkout through: +# https://github.com/pierrepeterlongo/commet/archive/master.zip +sources = [SOURCE_ZIP] +files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] + +pythonversion = '2.7.11' +versionsuffix = '-Python-%(pythonversion)s' + +dependencies = [ + ('Python', pythonversion), +] + +checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["Commet.py","bvop","compare_reads","extract_reads","filter_reads","index_and_search"]], + 'dirs' : ['doc','include'] +} + +moduleclass = 'bio' -- GitLab From 7ac6d46d9d2b1bf23b8bd44dd02adcd717c0b08f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 15:14:36 +0200 Subject: [PATCH 545/722] stick to freetype 2.6.2 for compatibility with matplotlib 1.5.1 --- .../p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb index dabb8b2f35..0fd64f3fd2 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'PIL' version = '1.1.7' -versionsuffix = '-Python-%(ppyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.pythonware.com/products/pil' description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. @@ -15,14 +15,11 @@ sources = ['Imaging-%(version)s.tar.gz'] patches = ['PIL-%(version)s-find-deps.patch'] -pyver = '2.7.11' -versionsuffix = '-Python-%s' % pyver dependencies = [ ('zlib', '1.2.8'), - ('Python', pyver), + ('Python', '2.7.11'), ('libjpeg-turbo', '1.4.2'), - # currently not used because of dependency hell - # ('freetype', '2.6.1'), + ('freetype', '2.6.2'), ] options = {'modulename': 'PIL'} -- GitLab From ab90ad2507bc8890a2aaa665e307cebe60f057d3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 15:29:11 +0200 Subject: [PATCH 546/722] fixed pyver --- .../c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb index 037900565c..abd2d674a6 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -3,6 +3,9 @@ easyblock = 'MakeCp' name = 'Commet' version = '20160422' +pyver = '2.7.11' +versionsuffix = '-Python-%(pyver)s' + homepage = 'https://colibread.inria.fr/software/commet/' description = """ COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. """ @@ -14,11 +17,9 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_ZIP] files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] -pythonversion = '2.7.11' -versionsuffix = '-Python-%(pythonversion)s' dependencies = [ - ('Python', pythonversion), + ('Python', pyver), ] checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] @@ -28,4 +29,4 @@ sanity_check_paths = { 'dirs' : ['doc','include'] } -moduleclass = 'bio' +moduleclass = 'bio' \ No newline at end of file -- GitLab From 3966bc3e025065c771252bae4528eee8d3c653e2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 15:52:23 +0200 Subject: [PATCH 547/722] CrossTalkZ with foss 2016a --- .../c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb new file mode 100644 index 0000000000..f798c72eb5 --- /dev/null +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CrossTalkZ' +version = '1.4' + +homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +description = """ +CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +] +sources = ['%(name)s_%(version)s.tgz'] + +dependencies = [('Boost', '1.60.0')] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" + +builddependencies = [('CMake', '3.4.3', '', ('foss','2016a'))] + +sanity_check_paths = { + 'files': ['bin/CrossTalkZ'], + 'dirs': [''], +} + +moduleclass = 'bio' \ No newline at end of file -- GitLab From a9a96a44eecdb03cc1396f86fd35ad79e5a8c2db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 16:02:37 +0200 Subject: [PATCH 548/722] add test configuration for Travis --- .travis.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000000..07d8498dcd --- /dev/null +++ b/.travis.yml @@ -0,0 +1,18 @@ +language: python +python: + - 2.6 + - 2.7 +addons: + apt: + packages: + - tcl8.5 +install: + # install easybuild-framework/easybuild-easyblocks (and dependencies) + # use 'develop' branch of framework/easyblocks, except when testing 'master' + if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz + - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz + # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework + - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT +script: + - python -O -m test.easyconfigs.suite -- GitLab From e23363ce6f9b632096702d193242e5221c5f7cc4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 22 Apr 2016 16:06:42 +0200 Subject: [PATCH 549/722] Fix failing FSL on RHEL 7 --- .../easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb | 4 ++-- .../easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch | 14 ++++++++++++++ 2 files changed, 16 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb index a26ad87936..5b9dfba11b 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb @@ -11,15 +11,15 @@ sources = ['%(namelower)s-%(version)s-sources.tar.gz'] patches = [ 'FSL-%(version)s_makefile_fixes.patch', + 'FSL-%(version)s_missing_lib.patch', 'FSL_icc_nan-inf_fix.patch', ] -preconfigopts = 'CFLAGS="-I%(builddir)s/src $CFLAGS"' - dependencies = [ ('freeglut', '3.0.0'), ('expat', '2.1.0'), ('libX11', '1.6.3'), + ('zlib', '1.2.8'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch new file mode 100644 index 0000000000..40e5baff2f --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch @@ -0,0 +1,14 @@ +# On RHEL 7 and friends, you need to link to libglapi too +# Ward Poelmans +diff -ur fsl.oirg/src/fslsurface/Makefile fsl/src/fslsurface/Makefile +--- fsl.oirg/src/fslsurface/Makefile 2014-02-24 12:09:05.000000000 +0100 ++++ fsl/src/fslsurface/Makefile 2016-04-21 18:03:50.246117983 +0200 +@@ -37,7 +37,7 @@ + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} + + +-LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass ++LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass -lglapi + + APPLY_ZLIB = -DHAVE_ZLIB + -- GitLab From 54f93414557afa15e4d1234300f5a0ca53ff46d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 17:37:00 +0200 Subject: [PATCH 551/722] add easyconfig i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb --- ...-1.0-20160213-intel-2016a-Python-2.7.11.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a0ac2c0885 --- /dev/null +++ b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name ='i-PI' +version = '1.0-20160213' +commit = '2a09a6d' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/i-pi/i-pi' +description = """A Python wrapper for (ab initio) (path integrals) molecular dynamics""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/i-pi/i-pi/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('Python', '2.7.11'), +] + +options = {'modulename': 'ipi'} + +sanity_check_paths = { + 'files': ['bin/i-pi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' -- GitLab From 48744e84a92f73b252f175f9925e0af41fc8f35a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 17:46:56 +0200 Subject: [PATCH 552/722] make dev version PEP440 compliant --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 72cf85df21..cf1d254d29 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.8.0dev0' +VERSION = '2.8.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 40f5979f3457df08f8f40f1afa54a122f9ad2ece Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 18:20:43 +0200 Subject: [PATCH 553/722] remove faulty PIL easyconfig --- ...PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb deleted file mode 100644 index 93ba3d3868..0000000000 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PIL' -version = '1.1.7' -versionsuffix = '-Python-%(ppyver)s' - -homepage = 'http://www.pythonware.com/products/pil' -description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. - This library supports many file formats, and provides powerful image processing and graphics capabilities.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://effbot.org/downloads/'] -sources = ['Imaging-%(version)s.tar.gz'] - -patches = ['PIL-%(version)s-find-deps.patch'] - -dependencies = [ - ('zlib', '1.2.8'), - ('Python', '2.7.11'), - ('libjpeg-turbo', '1.4.2'), - ('freetype', '2.6.3'), -] - -options = {'modulename': 'PIL'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], -} - -moduleclass = 'vis' -- GitLab From 3209fcc10eff09c48149a435a4d568b3a8e7a94d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:06:07 +0200 Subject: [PATCH 554/722] query GitHub for commit ID of framework/easyblocks branch being used --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 07d8498dcd..de7edac95e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,7 +10,9 @@ install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - curl -si https://api.github.com/repos/hpcugent/easybuild-framework/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz + - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT -- GitLab From e2387d1953bd9797547e5da2016e2ec1bf333897 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:12:42 +0200 Subject: [PATCH 555/722] fix typo --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index de7edac95e..9e395b922a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,7 +9,7 @@ addons: install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi - curl -si https://api.github.com/repos/hpcugent/easybuild-framework/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha -- GitLab From 643d94631fe876912443b51ad8eb7483da39c284 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:14:33 +0200 Subject: [PATCH 556/722] set $PYTHONPATH --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 9e395b922a..74257fabfb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,4 +17,5 @@ install: # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT script: + - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -- GitLab From 9a7580590297de695981ebf84c327abb39fff3b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:48:22 +0200 Subject: [PATCH 557/722] install python-graph-core library required by easyconfig tests --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 74257fabfb..47842a3535 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,6 +7,8 @@ addons: packages: - tcl8.5 install: + # required for test_dep_graph + - pip install python-graph-core # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi -- GitLab From d65154ee61c23a8fdc6583d5a66920fb9aae445b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 20:03:14 +0200 Subject: [PATCH 558/722] also install python-graph-dot --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 47842a3535..a67e42aebf 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,7 +8,7 @@ addons: - tcl8.5 install: # required for test_dep_graph - - pip install python-graph-core + - pip install python-graph-core python-graph-dot # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi -- GitLab From e2b1e2bf1eea6eeee0813e05dd8a0e6d004c76f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 22:29:53 +0200 Subject: [PATCH 559/722] remove Rust easyconfig using intel toolchain, rustc doesn't work --- .../r/Rust/Rust-1.8.0-intel-2016a.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb deleted file mode 100644 index e2f00427e8..0000000000 --- a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Rust' -version = '1.8.0' - -homepage = 'https://www.rust-lang.org' -description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, - and guarantees thread safety.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['https://static.rust-lang.org/dist/'] -sources = ['rustc-%(version)s-src.tar.gz'] - -builddependencies = [('Python', '2.7.11')] - -dependencies = [ - ('LLVM', '3.8.0'), -] - -configopts = "--llvm-root=$EBROOTLLVM" - -sanity_check_paths = { - 'files': ['bin/rustc', 'bin/rustdoc'], - 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], -} - -moduleclass = 'lang' -- GitLab From dea89b699b0c8bb51fd847f807d32b2285885326 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 23 Apr 2016 08:18:33 +0800 Subject: [PATCH 560/722] fix style --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index d06eb6d47f..d3ce57aec0 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -25,6 +25,8 @@ configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' +parallel = 1 + files_to_copy = [(['bin/*'], 'bin')] sanity_check_paths = { @@ -34,5 +36,3 @@ sanity_check_paths = { } moduleclass = 'phys' - -parallel = 1 -- GitLab From cf3fc8237183fa5f3bae7eb7e67089f11f3a4162 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 23 Apr 2016 10:29:18 +0200 Subject: [PATCH 561/722] also test with Lmod as modules tool on Travis --- .travis.yml | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index a67e42aebf..82661648a7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,7 +1,17 @@ language: python -python: - - 2.6 - - 2.7 +python: 2.6 +env: + matrix: + - ENV_MOD_VERSION=3.2.10 + - LMOD_VERSION=5.6.3 EASYBUILD_MODULES_TOOL=Lmod + - LMOD_VERSION=6.3.1 EASYBUILD_MODULES_TOOL=Lmod EASYBUILD_MODULE_SYNTAX=Lua +matrix: + # mark build as finished as soon as job has failed + fast_finish: true + include: + # also test default configuration with Python 2.7 + - python: 2.7 + env: ENV_MOD_VERSION=3.2.10 addons: apt: packages: @@ -17,7 +27,9 @@ install: - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT + - if [ ! -z $ENV_MOD_VERSION ]; then source $(which install_eb_dep.sh) modules-${ENV_MOD_VERSION} $HOME; fi + - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi + - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) Lmod-${LMOD_VERSION} $HOME; fi script: - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -- GitLab From 25e957fafed3d7db1f16375949d364e499a37747 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 13:09:49 +0200 Subject: [PATCH 562/722] long line fix --- .../c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb index abd2d674a6..0ddc0b62f9 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -25,8 +25,9 @@ dependencies = [ checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["Commet.py","bvop","compare_reads","extract_reads","filter_reads","index_and_search"]], - 'dirs' : ['doc','include'] + 'files': ["bin/%s" % binfile for binfile in ["Commet.py", "bvop", + "compare_reads", "extract_reads", "filter_reads", "index_and_search"]], + 'dirs' : ['doc', 'include'] } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From 92df775e7f99a7067490b356bcf00af058e51f60 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 13:14:34 +0200 Subject: [PATCH 563/722] style fixes --- .../Commet-20160422-foss-2016a-Python-2.7.11.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb index 0ddc0b62f9..2c16bccce7 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -7,7 +7,8 @@ pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' homepage = 'https://colibread.inria.fr/software/commet/' -description = """ COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. +description = """ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of +a large metagenomic project. """ toolchain = {'name': 'foss', 'version': '2016a'} @@ -15,15 +16,15 @@ toolchain = {'name': 'foss', 'version': '2016a'} # there is no tarball provided, only git checkout through: # https://github.com/pierrepeterlongo/commet/archive/master.zip sources = [SOURCE_ZIP] -files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] +checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] + +files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ] -checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] - sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["Commet.py", "bvop", "compare_reads", "extract_reads", "filter_reads", "index_and_search"]], -- GitLab From 5576182d21a0dfacf0aa8a1a9b990c254c7cf111 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 19:08:36 +0200 Subject: [PATCH 564/722] quickfixes --- .../Biopython-1.65-foss-2016a-Python-2.7.11.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index f4b92dace0..2abd2af08c 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -10,6 +10,8 @@ easyblock = "PythonPackage" name = 'Biopython' version = '1.65' +versionsuffix = "-Python-%(pyver)s" + homepage = 'http://www.biopython.org' description = """Biopython is a set of freely available tools for biological computation written @@ -22,20 +24,13 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://biopython.org/DIST'] sources = ['%(namelower)s-%(version)s.tar.gz'] -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = "-%(python)s-%(pyver)s" - dependencies = [ - (python, pyver) + ('Python', '2.7.11') ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/biopython-%(version)s-py%(pyshortver)s.egg-info'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', - 'lib/python%(pyshortver)s/site-packages/BioSQL'] + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] } options = {'modulename': 'Bio'} -- GitLab From 2c0e1b6d8ab6bc2727421dc4a8d214a886c2f516 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 19:31:05 +0200 Subject: [PATCH 565/722] quickfixes --- .../c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb index f798c72eb5..59c924d670 100644 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb @@ -5,11 +5,12 @@ version = '1.4' homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' description = """ -CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. +CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of +gene or protein groups in large biological networks. """ toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} +toolchainopts = {'usempi': True, 'pic': True} source_urls = [ 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' @@ -22,11 +23,11 @@ start_dir = 'src' configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" -builddependencies = [('CMake', '3.4.3', '', ('foss','2016a'))] +builddependencies = [('CMake', '3.4.3',)] sanity_check_paths = { 'files': ['bin/CrossTalkZ'], 'dirs': [''], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From 086c0dbb972a7084122b4b5eaf39da87a6bcaacb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 23 Apr 2016 23:56:48 +0100 Subject: [PATCH 566/722] Update SAMtools to 1.3.1 --- .../s/SAMtools/SAMtools-1.3.1-foss-2015b.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3.1-foss-2016a.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3.1-intel-2016a.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3.1_Makefile.patch | 24 ++++++++++++++ 4 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb new file mode 100644 index 0000000000..4ee9352c3d --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb new file mode 100644 index 0000000000..fea05c529c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb new file mode 100644 index 0000000000..d88f5e50e8 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch new file mode 100644 index 0000000000..c5b04c6958 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch @@ -0,0 +1,24 @@ +Common subdirectories: samtools-1.3.1/examples and samtools-1.3.1.new/examples +Common subdirectories: samtools-1.3.1/htslib-1.3.1 and samtools-1.3.1.new/htslib-1.3.1 +diff -u samtools-1.3.1/Makefile samtools-1.3.1.new/Makefile +--- samtools-1.3.1/Makefile 2016-04-22 10:51:16.000000000 +0100 ++++ samtools-1.3.1.new/Makefile 2016-04-23 23:53:26.266962157 +0100 +@@ -82,13 +82,13 @@ + # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally + ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz -ldl $(LIBS) ++ALL_LIBS = -L$(EBROOTZLIB)/lib -lz -ldl $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. + + config.mk: +- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3.1#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ ++ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3.1#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-L$$(EBROOTNCURSES)\/lib -lcurses/g' config.mk.in > $@ + + config.h: + echo '/* Basic config.h generated by Makefile */' > $@ +Common subdirectories: samtools-1.3.1/misc and samtools-1.3.1.new/misc +Common subdirectories: samtools-1.3.1/test and samtools-1.3.1.new/test +Common subdirectories: samtools-1.3.1/win32 and samtools-1.3.1.new/win32 -- GitLab From 2ab4d6d539228f0e637f1e5817cd9b983da10d7b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 24 Apr 2016 19:44:15 +0200 Subject: [PATCH 567/722] cutadapt with foss 2016a --- ...cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0a504a247d --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.9.1' +pyver = '2.7.11' +versionsuffix = '-Python-%(pyver)s' +pyshortver = '.'.join(pyver.split('.')[:2]) + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cutadapt/'], +} + +moduleclass = 'bio' -- GitLab From efb8760eacfd270bfefb526017504bc11f0bc3e7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 25 Apr 2016 11:57:53 +0200 Subject: [PATCH 568/722] libgtextutils with foss 2016a --- .../libgtextutils-0.7-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb new file mode 100644 index 0000000000..c1b5b27e46 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'libgtextutils' +version = '0.7' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/libgtextutils/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'lib' -- GitLab From 7fd4c7a674c4b93466fb96abf122f53e4dc3dbd5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 25 Apr 2016 11:59:57 +0200 Subject: [PATCH 569/722] FASTX-Toolket-0.0.14 with foss 2016a --- .../FASTX-Toolkit-0.0.14-foss-2016a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb new file mode 100644 index 0000000000..a69a7b9e2f --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['fastx_toolkit-%(version)s.tar.bz2'] + +builddependencies = [('libgtextutils', '0.7')] + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']], + 'dirs': ['.'] +} + +moduleclass = 'bio' -- GitLab From ee61831b0499b51bbb5684d61ec1772ffa0c1021 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 25 Apr 2016 12:00:17 +0200 Subject: [PATCH 570/722] Add Clang 3.8 --- .../c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb | 31 ++++++++++++ .../c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb | 50 +++++++++++++++++++ .../i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb | 21 ++++++++ .../l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb | 28 +++++++++++ .../n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb | 34 +++++++++++++ .../Python-2.7.11-GCC-4.9.3-2.25-bare.eb | 32 ++++++++++++ .../s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb | 41 +++++++++++++++ 7 files changed, 237 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..7c4301fdfe --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..23fe1ddcc9 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.8.0" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", + "openmp-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.0'), + ('ISL', '0.16'), +] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Python', '2.7.11', '-bare'), + ('libxml2', '2.9.3'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..6b38a91f39 --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.16' + +homepage = 'http://isl.gforge.inria.fr/' +description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GMP', '6.1.0')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..ba6d0a4c3f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..02e4aae6ca --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb new file mode 100644 index 0000000000..895d73b128 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb @@ -0,0 +1,32 @@ +name = 'Python' +version = '2.7.11' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3', '', ('GCCcore', '4.9.3')), + ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..5c86155323 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3', '', ('GCCcore', '4.9.3')), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' -- GitLab From bfca7b250a70b412b02b70921c158c85923ab215 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 25 Apr 2016 12:57:08 +0200 Subject: [PATCH 571/722] Fix conflict --- easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb index 7c4301fdfe..619aaa3ab8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' dependencies = [ - ('ncurses', '6.0'), + ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons #('OpenSSL', '1.0.1s'), -- GitLab From ebc6dc8fdd062abf4da5cbc1b71570b46f4cc211 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 26 Apr 2016 16:33:46 +0800 Subject: [PATCH 572/722] {chem}[intel/2016.02-GCC-4.9] pymatgen 3.5.10 and spglib 1.9.2 --- ...5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 33 +++++++++++++++++++ .../spglib-1.9.2-intel-2016.02-GCC-4.9.eb | 21 ++++++++++++ .../spglib-1.9.2_remove_duplicate.patch | 11 +++++++ 3 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb new file mode 100644 index 0000000000..cacf27ebc3 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '3.5.0' + +homepage = 'https://pypi.python.org/pypi/pymatgen' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +# source not in url PYPI_SOURCE ? +#source_urls = [PYPI_SOURCE] +source_urls = ['http://pypi.python.org/packages/7a/ae/c1bbe01227514bec203934d608c7319fec173791b3c58afa8e169affb976/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.11' + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('spglib', '1.9.2'), +] + +py_short_ver = '.'.join(pythonversion.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % py_short_ver], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..99c05961d7 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.9.2' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['spglib-1.9.2_remove_duplicate.patch'] + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch new file mode 100644 index 0000000000..c228aceb25 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch @@ -0,0 +1,11 @@ +--- src/Makefile.in.orig 2016-04-26 16:21:29.900203000 +0800 ++++ src/Makefile.in 2016-04-26 16:21:43.531192514 +0800 +@@ -562,7 +562,7 @@ + version.h + + libsymspg_la_SOURCES = $(spglib_c) $(spglib_h) +-pkginclude_HEADERS = $(spglib_h) debug.h ++pkginclude_HEADERS = $(spglib_h) + # libsymspg_la_LDFLAGS = -version-info 0:1:0 + libsymspg_la_LIBADD = -lm + spglib_test_SOURCES = test.c $(spglib_c) $(spglib_h) -- GitLab From 38ac1422594760bc4281382bd4f22bea36297de7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 17:33:32 +0200 Subject: [PATCH 573/722] fix use of resolve_dependencies in tests --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f3b329c872..db5060f0b6 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -113,7 +113,7 @@ class EasyConfigTest(TestCase): if dep.get('external_module', False): ec['dependencies'].remove(dep) - self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, retain_all_deps=True) + self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, modules_tool(), retain_all_deps=True) def test_dep_graph(self): """Unit test that builds a full dependency graph.""" -- GitLab From 4df336393a0094535ed365c30f094d682a2a9bd2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 17:37:38 +0200 Subject: [PATCH 574/722] add easyconfig travis-1.8.2-Ruby-2.3.1.eb, add easyconfig Ruby-2.3.1.eb --- easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb | 63 +++++++++++++++++++ .../t/travis/travis-1.8.2-Ruby-2.3.1.eb | 24 +++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb create mode 100644 easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb new file mode 100644 index 0000000000..873541fd42 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb @@ -0,0 +1,63 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.3.1' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +ext_options = { + 'source_urls': ['http://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_list = [ + ('ffi', '1.9.10', ext_options), + ('childprocess', '0.5.9', ext_options), + ('json', '1.8.3', ext_options), + ('cabin', '0.8.1', ext_options), + ('backports', '3.6.8', ext_options), + ('arr-pm', '0.0.10', ext_options), + ('clamp', '1.0.0', ext_options), + ('multipart-post', '2.0.0', ext_options), + ('faraday', '0.9.2', ext_options), + ('faraday_middleware', '0.10.0', ext_options), + ('highline', '1.7.8', ext_options), + ('net-http-pipeline', '1.0.1', ext_options), + ('net-http-persistent', '2.9.4', ext_options), + ('multi_json', '1.11.3', ext_options), + ('addressable', '2.4.0', ext_options), + ('gh', '0.14.0', ext_options), + ('launchy', '2.4.3', ext_options), + ('ethon', '0.8.1', ext_options), + ('typhoeus', '0.8.0', ext_options), + ('websocket', '1.2.3', ext_options), + ('pusher-client', '0.6.2', ext_options), + ('diff-lcs', '1.2.5', ext_options), + ('rspec-support', '3.4.1', ext_options), + ('rspec-mocks', '3.4.1', ext_options), + ('rspec-expectations', '3.4.0', ext_options), + ('rspec-core', '3.4.4', ext_options), + ('rspec', '3.4.0', ext_options), + ('rack', '1.6.4', ext_options), + ('rack-protection', '1.5.3', ext_options), + ('tilt', '2.0.2', ext_options), + ('sinatra', '1.4.7', ext_options), + ('rack-test', '0.6.3', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb b/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb new file mode 100644 index 0000000000..ebac3ec2d3 --- /dev/null +++ b/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb @@ -0,0 +1,24 @@ +easyblock = 'RubyGem' + +name = 'travis' +version = '1.8.2' + +rubyver = '2.3.1' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://github.com/travis-ci/travis.rb' +description = """Travis CI Client (CLI and Ruby library)""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://rubygems.org/downloads/'] +sources = ['%(namelower)s-%(version)s.gem'] + +dependencies = [('Ruby', rubyver)] + +sanity_check_paths = { + 'files': ['bin/travis'], + 'dirs': ['gems/travis-%(version)s/lib/travis'], +} + +moduleclass = 'tools' -- GitLab From 0e7e6ad93bed78ec974e24ad4e697a16f4e6a90c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 19:37:42 +0200 Subject: [PATCH 575/722] install easybuild-framework & easybuild-easyblocks via git clone && easy_install --- .travis.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 82661648a7..00f7860f26 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,10 +22,12 @@ install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi - - curl -si https://api.github.com/repos/hpcugent/easybuild-framework/git/refs/heads/${BRANCH} | grep sha - - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz - - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha - - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz + - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-framework.git + - cd easybuild-framework; git log -n 1; cd - + - easy_install $PWD/easybuild-framework + - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-easyblocks.git + - cd easybuild-easyblocks; git log -n 1; cd - + - easy_install $PWD/easybuild-easyblocks # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - if [ ! -z $ENV_MOD_VERSION ]; then source $(which install_eb_dep.sh) modules-${ENV_MOD_VERSION} $HOME; fi - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi -- GitLab From 40a6f5d08a0399cc544dd39ba8145a345e4a3414 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 19:55:13 +0200 Subject: [PATCH 576/722] fix cwd when cloning --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 00f7860f26..127edacd18 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,6 +22,7 @@ install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - cd $HOME - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-framework.git - cd easybuild-framework; git log -n 1; cd - - easy_install $PWD/easybuild-framework -- GitLab From fe83740c235f48de4924f02e3a463cce5adc1d68 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 26 Apr 2016 21:39:01 +0100 Subject: [PATCH 577/722] Add patch information and apply more macros --- .../easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb | 4 +++- .../easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb | 4 +++- .../easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb | 4 +++- .../easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch | 8 +++----- 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb index 4ee9352c3d..a7026c36d0 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb @@ -6,6 +6,8 @@ # License:: MIT/GPL # $Id$ # +# Modified by: Adam Huffman +# The Francis Crick Institute ## name = 'SAMtools' version = '1.3.1' @@ -21,7 +23,7 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve sources = [SOURCELOWER_TAR_BZ2] # Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-1.3.1_Makefile.patch'] +patches = ['SAMtools-%(version)s_Makefile.patch'] dependencies = [ ('ncurses', '5.9'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb index fea05c529c..7fa65122da 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb @@ -6,6 +6,8 @@ # License:: MIT/GPL # $Id$ # +# Modified by: Adam Huffman +# The Francis Crick Institute ## name = 'SAMtools' version = '1.3.1' @@ -21,7 +23,7 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve sources = [SOURCELOWER_TAR_BZ2] # Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-1.3.1_Makefile.patch'] +patches = ['SAMtools-%(version)s_Makefile.patch'] dependencies = [ ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb index d88f5e50e8..91ca187c34 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb @@ -6,6 +6,8 @@ # License:: MIT/GPL # $Id$ # +# Modified by: Adam Huffman +# The Francis Crick Institute ## name = 'SAMtools' version = '1.3.1' @@ -21,7 +23,7 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve sources = [SOURCELOWER_TAR_BZ2] # Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-1.3.1_Makefile.patch'] +patches = ['SAMtools-%(version)s_Makefile.patch'] dependencies = [ ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch index c5b04c6958..4d74b2e9b1 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch @@ -1,5 +1,6 @@ -Common subdirectories: samtools-1.3.1/examples and samtools-1.3.1.new/examples -Common subdirectories: samtools-1.3.1/htslib-1.3.1 and samtools-1.3.1.new/htslib-1.3.1 +# Use EB modules for zlib and ncurses +# Author: Adam Huffman +# The Francis Crick Institute diff -u samtools-1.3.1/Makefile samtools-1.3.1.new/Makefile --- samtools-1.3.1/Makefile 2016-04-22 10:51:16.000000000 +0100 +++ samtools-1.3.1.new/Makefile 2016-04-23 23:53:26.266962157 +0100 @@ -19,6 +20,3 @@ diff -u samtools-1.3.1/Makefile samtools-1.3.1.new/Makefile config.h: echo '/* Basic config.h generated by Makefile */' > $@ -Common subdirectories: samtools-1.3.1/misc and samtools-1.3.1.new/misc -Common subdirectories: samtools-1.3.1/test and samtools-1.3.1.new/test -Common subdirectories: samtools-1.3.1/win32 and samtools-1.3.1.new/win32 -- GitLab From 5145c090f795ab0ef73ae3c6d5b6fe91dc6ab847 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 26 Apr 2016 21:42:56 +0100 Subject: [PATCH 578/722] Second attempt at MuTect update to 1.1.7 --- .../m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb new file mode 100644 index 0000000000..fb72a09f73 --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Version 1.1.7 modified by +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'MuTect' +version = '1.1.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +# Need to be logged in to download, at this URL +# source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +sources = ['muTect-%(version)s-bin.zip'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ["muTect-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +""" + +moduleclass = 'bio' -- GitLab From 41ccd5905b4c848474c5c1744cf05d0b97e607c5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 26 Apr 2016 21:52:42 +0100 Subject: [PATCH 579/722] Cleanup macros and provide legacy version --- .../v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 30 +++++++++++++++++++ .../v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb | 11 +++---- 2 files changed, 36 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb new file mode 100644 index 0000000000..db71fa9969 --- /dev/null +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = 'JAR' + +name = 'VarScan' +version = '2.3.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://varscan.sourceforge.net/' +description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [('%(name)s.v%(version)s.jar', 'download')] +source_urls = ['https://sourceforge.net/projects/varscan/files/'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +modloadmsg = """ +to execute: java -jar \\$EBROOTVARSCAN/VarScan.v%(version)s.jar +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb index 36d97df090..186dfc58cc 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb @@ -6,6 +6,7 @@ easyblock = 'JAR' name = 'VarScan' version = '2.4.1' +versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/dkoboldt/varscan' description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" @@ -15,15 +16,15 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['%(name)s.v%(version)s.jar'] source_urls = ['https://github.com/dkoboldt/varscan/releases/download/v%(version)s'] -java = 'Java' -javaver = '1.7.0_80' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] +dependencies = [('Java', '1.7.0_80')] sanity_check_paths = { 'files': sources, 'dirs': [], } +modloadmsg = """ +to execute: java -jar \\$EBROOTVARSCAN/VarScan.v%(version)s.jar +""" + moduleclass = 'bio' -- GitLab From bede2f51f66ffd99701e4b03c1b94b94a51aaa60 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 11:39:01 +0800 Subject: [PATCH 580/722] add comment to patch --- .../easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch index c228aceb25..8382a4ebe3 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch @@ -1,3 +1,5 @@ +debug.h is already in $(spglib_h), which causes make install to fail +author: Miguel Dias Costa (National University of Singapore) --- src/Makefile.in.orig 2016-04-26 16:21:29.900203000 +0800 +++ src/Makefile.in 2016-04-26 16:21:43.531192514 +0800 @@ -562,7 +562,7 @@ -- GitLab From c0b8bf724521669e0d3d03746c38ab85d9e3e02d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 12:05:19 +0800 Subject: [PATCH 581/722] use pyshortver template --- .../pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index cacf27ebc3..786e233e0c 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -9,7 +9,7 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -# source not in url PYPI_SOURCE ? +# source package not (yet?) in url PYPI_SOURCE #source_urls = [PYPI_SOURCE] source_urls = ['http://pypi.python.org/packages/7a/ae/c1bbe01227514bec203934d608c7319fec173791b3c58afa8e169affb976/'] sources = [SOURCE_TAR_GZ] @@ -24,10 +24,9 @@ dependencies = [ ('spglib', '1.9.2'), ] -py_short_ver = '.'.join(pythonversion.split('.')[:2]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages' % py_short_ver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] } moduleclass = 'chem' -- GitLab From f716f392e6b4b4c6b613e468d5bf07ab021cbbc2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 12:20:13 +0800 Subject: [PATCH 582/722] use && instead of ; between commands --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index c0d639cc89..5afb842c80 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -17,7 +17,7 @@ checksums = ['8740562da41e87a62eb8d457675e4bfd'] skipsteps = ['configure'] -prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 4700de27c4..9d064dae20 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -17,7 +17,7 @@ checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] skipsteps = ['configure'] -prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' -- GitLab From 4134e68be75d60ac1889c06af12238baa54fe69b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 27 Apr 2016 09:20:12 +0200 Subject: [PATCH 583/722] Remove redundant easyconfig --- .../n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb deleted file mode 100644 index 02e4aae6ca..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '6.0' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' -- GitLab From f1a4154428e398d2c45117c91b6cd62af1806829 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 16:31:43 +0800 Subject: [PATCH 584/722] fix style --- ...tgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 12 +++--------- .../s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 786e233e0c..f6c2197ee2 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = "PythonPackage" name = 'pymatgen' version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/pymatgen' description = """Python Materials Genomics is a robust materials analysis code that defines core object @@ -9,18 +10,11 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -# source package not (yet?) in url PYPI_SOURCE -#source_urls = [PYPI_SOURCE] -source_urls = ['http://pypi.python.org/packages/7a/ae/c1bbe01227514bec203934d608c7319fec173791b3c58afa8e169affb976/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = 'Python' -pythonversion = '2.7.11' - -versionsuffix = '-%s-%s' % (python, pythonversion) - dependencies = [ - (python, pythonversion), + ('Python', '2.7.11'), ('spglib', '1.9.2'), ] diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb index 99c05961d7..8451bf0c50 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['spglib-1.9.2_remove_duplicate.patch'] +patches = ['spglib-%(version)s_remove_duplicate.patch'] sanity_check_paths = { 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], -- GitLab From 435eab2e07d7f781915cb672792e3ed0506dfa96 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 10:04:20 +0100 Subject: [PATCH 585/722] Don't specify version for dummy toolchain --- easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb index db71fa9969..ba30d5877f 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -11,7 +11,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://varscan.sourceforge.net/' description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [('%(name)s.v%(version)s.jar', 'download')] source_urls = ['https://sourceforge.net/projects/varscan/files/'] -- GitLab From a9193aaca3032ffc844843556cba05e5957a3382 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 11:38:17 +0200 Subject: [PATCH 586/722] add easyconfig netCDF-Fortran-4.4.3-intel-2016a.eb --- .../netCDF-Fortran-4.4.3-intel-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb new file mode 100644 index 0000000000..4b898dd0fe --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb @@ -0,0 +1,19 @@ +name = 'netCDF-Fortran' +version = '4.4.3' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-fortran/archive/' +] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' -- GitLab From 0ff3e40f352c19ec30bc19fac917588e318ba4fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 11:38:47 +0200 Subject: [PATCH 587/722] add easyconfig tcsh-6.19.00-intel-2016a.eb --- .../t/tcsh/tcsh-6.19.00-intel-2016a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb new file mode 100644 index 0000000000..4a02bab4b4 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.19.00' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 45e20dbc351d80c93701dfc2fa9231d99019607f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 11:39:16 +0200 Subject: [PATCH 588/722] add easyconfig JasPer-1.900.1-intel-2016a.eb --- .../j/JasPer/JasPer-1.900.1-intel-2016a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb new file mode 100644 index 0000000000..ea3c592427 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' -- GitLab From 7f749b704350f3618123f17349c3b2599408bbbd Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 11:56:43 +0100 Subject: [PATCH 589/722] Use new download URL and apply new Java macros to existing 1.1.4 easyconfig --- .../m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb | 15 ++++---- .../m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 37 ------------------- 2 files changed, 8 insertions(+), 44 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index 1434f1c176..b7e4fa9091 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -2,11 +2,15 @@ # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +# Modified by +# Adam Huffman +# The Francis Crick Institute easyblock = 'Tarball' name = 'MuTect' version = '1.1.4' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' description = """ MuTect is a method developed at the Broad Institute for the reliable @@ -15,14 +19,11 @@ description = """ MuTect is a method developed at the Broad Institute for the re toolchain = {'name': 'dummy', 'version': ''} -source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +# Need to be logged in to download, at this URL +# source_urls = ['http://www.broadinstitute.org/cancer/cga/mutect_download'] sources = ['muTect-%(version)s-bin.zip'] -java = 'Java' -javaver = '1.7.0_80' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] +dependencies = [('Java', '1.7.0_80')] sanity_check_paths = { 'files': ["muTect-%(version)s.jar"], @@ -30,7 +31,7 @@ sanity_check_paths = { } modloadmsg = """ -to execute: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar """ moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb deleted file mode 100644 index fb72a09f73..0000000000 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb +++ /dev/null @@ -1,37 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# Version 1.1.7 modified by -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'Tarball' - -name = 'MuTect' -version = '1.1.7' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' -description = """ MuTect is a method developed at the Broad Institute for the reliable - and accurate identification of somatic point mutations in next generation sequencing - data of cancer genomes. """ - -toolchain = {'name': 'dummy', 'version': ''} - -# Need to be logged in to download, at this URL -# source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] -sources = ['muTect-%(version)s-bin.zip'] - -dependencies = [('Java', '1.7.0_80')] - -sanity_check_paths = { - 'files': ["muTect-%(version)s.jar"], - 'dirs': [], -} - -modloadmsg = """ -To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar -""" - -moduleclass = 'bio' -- GitLab From 836bced923277203a737f146a839a8fd491ea0cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 13:39:28 +0200 Subject: [PATCH 590/722] add easyconfig ParMETIS-4.0.3-intel-2016a.eb, add easyconfig METIS-5.1.0-intel-2016a-32bitIDX.eb, add easyconfig SCOTCH-6.0.4-intel-2016a.eb, add easyconfig ParMGridGen-1.0-intel-2016a.eb, add easyconfig OpenFOAM-Extend-3.2-intel-2016a.eb, add easyconfig numactl-2.0.11-intel-2016a.eb, add easyconfig hwloc-1.11.3-intel-2016a.eb --- .../h/hwloc/hwloc-1.11.3-intel-2016a.eb | 23 +++++++++ .../METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb | 24 ++++++++++ .../n/numactl/numactl-2.0.11-intel-2016a.eb | 23 +++++++++ .../OpenFOAM-Extend-3.2-intel-2016a.eb | 48 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb | 22 +++++++++ .../ParMGridGen-1.0-intel-2016a.eb | 27 +++++++++++ .../s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb | 14 ++++++ 7 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb new file mode 100644 index 0000000000..aad28dd23b --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb new file mode 100644 index 0000000000..a9aa0626e9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb @@ -0,0 +1,24 @@ +name = 'METIS' +version = '5.1.0' +# default 32-bit IDTYPEWIDTH, no patch used +versionsuffix = '-32bitIDX' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.5.2')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb new file mode 100644 index 0000000000..6379096747 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb new file mode 100644 index 0000000000..00e9eaf007 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'EB_OpenFOAM' + +name = 'OpenFOAM-Extend' +version = '3.2' + +homepage = 'http://www.extend-project.de/' +description = """OpenFOAM is a free, open source CFD software package. +OpenFOAM has an extensive range of features to solve anything from complex fluid flows +involving chemical reactions, turbulence and heat transfer, +to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-%(version)s/archive'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'OpenFOAM-Extend-%(version)s-ParMGridGen.patch', + 'OpenFOAM-Extend-3.1_build-qa.patch', + 'OpenFOAM-Extend-3.1_comp-mpi.patch', + 'OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch', +] + +dependencies = [ + ('hwloc', '1.11.3'), + ('ParMETIS', '4.0.3'), + ('METIS', '5.1.0', '-32bitIDX'), # order matters, METIS need to be listed after ParMETIS to get $CPATH right + ('SCOTCH', '6.0.4'), + ('Mesquite', '2.3.0'), + ('ParMGridGen', '1.0'), + ('Python', '2.7.11'), + # Libccmio v2.6.1, zoltan v3.5 +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('M4', '1.4.17'), + ('CMake', '3.5.2'), +] + +prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) + +# too many builds in parallel actually slows down the build +maxparallel = 4 + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb new file mode 100644 index 0000000000..d1d34fb057 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, + meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes + routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in + ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning + schemes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.5.2')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb new file mode 100644 index 0000000000..081f188ad5 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'ParMGridGen' +version = '1.0' + +homepage = 'http://www-users.cs.umn.edu/~moulitsa/software.html' +description = """ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, + that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited + for geometric multigrid methods.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://www-users.cs.umn.edu/~moulitsa/download/'] +sources = [SOURCE_TAR_GZ] + +patches = ['ParMGridGen-1.0_malloc_include.patch'] + +buildopts = 'parallel CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' + +files_to_copy = [ + (['MGridGen/Programs/mgridgen', 'ParMGridGen/Programs/parmgridgen'], 'bin'), + (['mgridgen.h', 'parmgridgen.h'], 'include'), + (['libmgrid.a', 'libparmgrid.a'], 'lib'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb new file mode 100644 index 0000000000..a90bb75fa5 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb @@ -0,0 +1,14 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' -- GitLab From 34b5d5abfa255f3464ce6dabefc279d14b2b67e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 13:44:11 +0200 Subject: [PATCH 591/722] add easyconfig JAGS-4.2.0-intel-2016a.eb --- .../j/JAGS/JAGS-4.2.0-intel-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb new file mode 100644 index 0000000000..1474dde18b --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.2.0' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [('http://sourceforge.net/projects/mcmc-jags/files/JAGS/%(version_major)s.x/Source/', 'download')] +sources = [SOURCE_TAR_GZ] + +configopts = ' --with-blas="-lmkl" --with-lapack="-lmkl" ' + +sanity_check_paths = { + 'files': ["bin/jags", "libexec/jags-terminal", "lib/libjags.%s" % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/JAGS', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' -- GitLab From cb092140059005c5fc0468dfb57ad2b5b4f04726 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 14:03:24 +0200 Subject: [PATCH 592/722] add easyconfig Mesquite-2.3.0-intel-2016a.eb --- .../m/Mesquite/Mesquite-2.3.0-intel-2016a.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb new file mode 100644 index 0000000000..fd518b2227 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'Mesquite' +version = '2.3.0' + +homepage = 'https://software.sandia.gov/mesquite/' +description = """Mesh-Quality Improvement Library""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://software.sandia.gov/mesquite/'] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'math' -- GitLab From 7bb25d33b0db30e01c8e995fdc0c3c4df76a5769 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 14:13:13 +0100 Subject: [PATCH 593/722] Clean up download URL --- easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index b7e4fa9091..0d2d28d47b 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -20,7 +20,7 @@ description = """ MuTect is a method developed at the Broad Institute for the re toolchain = {'name': 'dummy', 'version': ''} # Need to be logged in to download, at this URL -# source_urls = ['http://www.broadinstitute.org/cancer/cga/mutect_download'] +# http://www.broadinstitute.org/cancer/cga/mutect_download sources = ['muTect-%(version)s-bin.zip'] dependencies = [('Java', '1.7.0_80')] -- GitLab From 7706f3436e6b061846889c767616bfb3dbce8478 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 15:53:30 +0200 Subject: [PATCH 594/722] {geo}[intel/2016a] WRF 3.8 --- .../w/WRF/WRF-3.8-intel-2016a-dmpar.eb | 39 +++ ...F-3.8.0_netCDF-Fortran_separate_path.patch | 225 ++++++++++++++++++ 2 files changed, 264 insertions(+) create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb new file mode 100644 index 0000000000..8afc4ff822 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb @@ -0,0 +1,39 @@ +name = 'WRF' +version = '3.8.0' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version_major_minor)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.19.00')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.3'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF_tests_limit-runtimes.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch new file mode 100644 index 0000000000..f46ae78e87 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch @@ -0,0 +1,225 @@ +add support for using netCDF and netCDF-Fortran installations in separate paths +author: Kenneth Hoste (HPC-UGent) +diff -ru WRFV3.orig/arch/Config_new.pl WRFV3/arch/Config_new.pl +--- WRFV3.orig/arch/Config_new.pl 2015-12-11 19:38:11.000000000 +0100 ++++ WRFV3/arch/Config_new.pl 2016-04-27 12:07:59.419553000 +0200 +@@ -8,6 +8,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib may be in a different path + $sw_pnetcdf_path = "" ; + $sw_hdf5_path=""; + $sw_phdf5_path=""; +@@ -87,6 +88,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -114,6 +119,7 @@ + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { + $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -417,6 +423,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; + $_ =~ s/CONFIGURE_PHDF5_PATH/$sw_phdf5_path/g ; +Only in WRFV3/arch: Config_new.pl.orig +diff -ru WRFV3.orig/arch/configure_new.defaults WRFV3/arch/configure_new.defaults +--- WRFV3.orig/arch/configure_new.defaults 2016-02-29 07:22:29.000000000 +0100 ++++ WRFV3/arch/configure_new.defaults 2016-04-27 12:07:59.429182000 +0200 +@@ -1626,6 +1626,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +Only in WRFV3/arch: configure_new.defaults.orig +diff -ru WRFV3.orig/arch/conf_tokens WRFV3/arch/conf_tokens +--- WRFV3.orig/arch/conf_tokens 2008-02-26 16:39:38.000000000 +0100 ++++ WRFV3/arch/conf_tokens 2016-04-27 12:07:59.435906000 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -ru WRFV3.orig/arch/postamble_new WRFV3/arch/postamble_new +--- WRFV3.orig/arch/postamble_new 2016-02-05 22:22:09.000000000 +0100 ++++ WRFV3/arch/postamble_new 2016-04-27 12:08:58.368686000 +0200 +@@ -45,6 +45,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ + -I$(NETCDFPATH)/include \ ++ -I$(NETCDFFPATH)/include \ + CONFIGURE_RTTOV_INC + REGISTRY = Registry + CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE +@@ -67,6 +68,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH +++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + PNETCDFPATH = CONFIGURE_PNETCDF_PATH +@@ -97,7 +99,7 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + +Only in WRFV3/arch: postamble_new.orig +Only in WRFV3/arch: postamble_new.rej +diff -ru WRFV3.orig/configure WRFV3/configure +--- WRFV3.orig/configure 2015-12-11 19:38:11.000000000 +0100 ++++ WRFV3/configure 2016-04-27 12:58:24.475136000 +0200 +@@ -287,16 +287,28 @@ + USENETCDFF="" # see below + if [ -n "$NETCDF" ] ; then + echo "Will use NETCDF in dir: $NETCDF" ++ # for netCDF 4.2 and greater, the Fortran library is a separate install ++ if [ -z "$NETCDFF" ]; then ++ NETCDFF="$NETCDFF" ++ fi + # Oh UNIDATA, why make it so hard ... + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" ] ; then + USENETCDFF="-lnetcdff" + else +- USENETCDFF=" " ++ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++ else ++ USENETCDFF=" " ++ fi + fi + if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else +- USENETCDF=" " ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then ++ USENETCDF="-L$NETCDF/lib!-L$NETCDF/lib64!-lnetcdf" # ! will be replaced with space ++ else ++ USENETCDF=" " ++ fi + fi + else + echo "Will configure for use without NetCDF" +@@ -595,7 +607,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure_new.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config_new.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -707,10 +719,10 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure_new.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + echo + if test -n "$NETCDF4" ; then +@@ -719,7 +731,7 @@ + fi + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +Only in WRFV3: configure.orig +Only in WRFV3: configure.rej +diff -ru WRFV3.orig/external/io_netcdf/makefile WRFV3/external/io_netcdf/makefile +--- WRFV3.orig/external/io_netcdf/makefile 2014-07-13 01:39:10.000000000 +0200 ++++ WRFV3/external/io_netcdf/makefile 2016-04-27 12:07:59.490731000 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -ru WRFV3.orig/Makefile WRFV3/Makefile +--- WRFV3.orig/Makefile 2016-03-11 18:47:37.000000000 +0100 ++++ WRFV3/Makefile 2016-04-27 12:09:30.391608000 +0200 +@@ -867,7 +867,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) framework; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" FC="$(FC) $(FCBASEOPTS)" RANLIB="$(RANLIB)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" FC="$(SFC) $(FCBASEOPTS)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ + ESMF_MOD_DEPENDENCE="$(ESMF_MOD_DEPENDENCE)" AR="INTERNAL_BUILD_ERROR_SHOULD_NOT_NEED_AR" diffwrf; \ +Only in WRFV3: Makefile.orig +Only in WRFV3: Makefile.rej -- GitLab From 4734e785722c5b78cd0fe7420776439273e22727 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 16:14:00 +0200 Subject: [PATCH 595/722] fix easyconfig filename --- ...RF-3.8-intel-2016a-dmpar.eb => WRF-3.8.0-intel-2016a-dmpar.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/w/WRF/{WRF-3.8-intel-2016a-dmpar.eb => WRF-3.8.0-intel-2016a-dmpar.eb} (100%) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb rename to easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb -- GitLab From 39ddf5a97d55a5b9248c9bf3916d1b9fb41f8513 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 15:14:27 +0100 Subject: [PATCH 596/722] Update MuTect for 1.1.7 from new download site --- .../m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb new file mode 100644 index 0000000000..86bd5019e2 --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'MuTect' +version = '1.1.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +# Need to be logged in to download, at this URL +# and to click the checkbox to agree to the licence +# https://www.broadinstitute.org/gatk/download/auth?package=MuTect +sources = ['%(namelower)s-%(version)s.jar.zip'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ["%(namelower)s-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +To start MuTect: java -jar \\$EBROOTMUTECT/%(namelower)s-%(version)s.jar +""" + +moduleclass = 'bio' -- GitLab From 16218db65d867ab958db13dcbe99fcbf93724337 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2016 11:32:51 +0200 Subject: [PATCH 597/722] add dependency extensions for MarkupSafe and jsonscheme in IPython 3.2.3 easyconfigs --- .../i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb | 9 +++++++++ .../i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb index 693b2889a6..440fcbb412 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb @@ -52,9 +52,18 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb index e3341fcf31..7cf61546f1 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb @@ -52,9 +52,18 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), -- GitLab From d5d14e4f772188d6772c1dd9f3453ccc2725845c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2016 11:28:48 +0200 Subject: [PATCH 598/722] add vcversioner and functiools32 dependencies for jsonscheme in IPython easyconfig --- .../i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb index f70668f24c..5a7a6fc6ee 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -50,10 +50,16 @@ exts_list = [ }), ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], - }), + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), -- GitLab From 364ccf36a72ed191b8641e62239e7f924f228a1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2016 11:35:26 +0200 Subject: [PATCH 599/722] use %(pyver)s and %(pyshortver)s in IPython 3.2.3 easyconfigs --- .../IPython-3.2.3-foss-2015a-Python-2.7.11.eb | 12 ++++-------- .../IPython-3.2.3-intel-2015b-Python-2.7.10.eb | 12 ++++-------- 2 files changed, 8 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb index 440fcbb412..59f875819a 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'IPython' version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -13,13 +14,8 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'foss', 'version': '2015a'} -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.11'), ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), ] @@ -82,11 +78,11 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb index 7cf61546f1..4c8be19f1d 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'IPython' version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -13,13 +14,8 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015b'} -python = 'Python' -pyver = '2.7.10' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.10'), ('PyZMQ', '15.1.0', '%s-zmq4' % versionsuffix), ] @@ -82,11 +78,11 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ -- GitLab From 699e52ba961e329166861b28967659ef5284534b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 28 Apr 2016 14:51:54 +0200 Subject: [PATCH 600/722] dropped (new)lines --- .../c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb index 0a504a247d..5c57e5846c 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -9,9 +9,7 @@ easyblock = "PythonPackage" name = 'cutadapt' version = '1.9.1' -pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' -pyshortver = '.'.join(pyver.split('.')[:2]) homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and @@ -22,7 +20,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] - dependencies = [ ('Python', '2.7.11'), ] -- GitLab From 4b3f26cdb67eae384e941d5a9358502f27376475 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 28 Apr 2016 14:55:11 +0200 Subject: [PATCH 601/722] Version fix --- .../c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb new file mode 100644 index 0000000000..444de341bf --- /dev/null +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'CrossTalkZ' +version = '1.4' + +homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +description = """ +CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment +between pairs of gene or protein groups in large biological networks. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +] +sources = ['%(name)s_%(version)s.tgz'] + +dependencies = [('Boost', '1.60.0')] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" + +builddependencies = [('CMake', '3.4.3',)] + +sanity_check_paths = { + 'files': ['bin/CrossTalkZ'], + 'dirs': [''], +} + +moduleclass = 'bio' -- GitLab From 1f5400281627eb85afc587878f025e95fe58e9d5 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 28 Apr 2016 10:37:28 -0400 Subject: [PATCH 602/722] remove easyblock specification. it's not necessary --- .../easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb index cd9274f066..7bcbf378aa 100644 --- a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_libQGLViewer' - name = 'libQGLViewer' version = '2.6.3' -- GitLab From 4b632a70fb083454a252435f93947990715fce77 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 28 Apr 2016 16:42:26 +0200 Subject: [PATCH 603/722] remove 1.0 version --- .../c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb deleted file mode 100644 index 59c924d670..0000000000 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'CrossTalkZ' -version = '1.4' - -homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' -description = """ -CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of -gene or protein groups in large biological networks. -""" - -toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = [ - 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' -] -sources = ['%(name)s_%(version)s.tgz'] - -dependencies = [('Boost', '1.60.0')] - -start_dir = 'src' - -configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" - -builddependencies = [('CMake', '3.4.3',)] - -sanity_check_paths = { - 'files': ['bin/CrossTalkZ'], - 'dirs': [''], -} - -moduleclass = 'bio' -- GitLab From 34c2d2a3f23f82a1584528664c4efd174ffd5c04 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 28 Apr 2016 23:22:11 +0100 Subject: [PATCH 604/722] add easyconfig cramtools-3.0-Java-1.7.0_80.eb --- .../cramtools/cramtools-3.0-Java-1.7.0_80.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb new file mode 100644 index 0000000000..d00a912e71 --- /dev/null +++ b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'cramtools' +version = '3.0' +versionsuffix = "-Java-%(javaver)s" + +homepage = 'https://github.com/enasequence/cramtools/' +description = """CRAMTools is a set of Java tools and APIs for efficient compression of sequence +read data. Although this is intended as a stable version the code is released as +early access. Parts of the CRAMTools are experimental and may not be supported +in the future.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/enasequence/%(name)s/archive/'] + +dependencies = [('Java', '1.7.0_80')] + +modloadmsg = "To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" + +sanity_check_paths = { + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': ["lib"] +} + +moduleclass = 'bio' -- GitLab From 942f96a8f5f8a5b8b2586aa101d78ab815598490 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 28 Apr 2016 22:18:01 -0400 Subject: [PATCH 605/722] add PyGTS easyconfig with foss 2016a toolchain --- .../PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..d74951a2d3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyGTS' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourceforge.net/projects/pygts/' +description = """ PyGTS is a python package used to construct, manipulate, + and perform computations on triangulated surfaces. + It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('GLib', '2.47.5'), + ('GTS' ,'0.7.6'), + ('numpy', '1.8.2', versionsuffix), +] + +options = {'modulename': 'gts'} + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], + 'dirs':[], +} + +moduleclass = 'vis' -- GitLab From 38eb196e7de2b754a1c0205e11df8a50d9b2075b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 15:30:02 +0200 Subject: [PATCH 606/722] add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being used --- ...tplotlib-1.5.1-foss-2015b-Python-2.7.10.eb | 1 + ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 1 + ...plotlib-1.5.1-intel-2015b-Python-2.7.11.eb | 1 + ...plotlib-1.5.1-intel-2016a-Python-2.7.11.eb | 1 + ...tplotlib-1.5.1-intel-2016a-Python-3.5.1.eb | 1 + .../matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch | 26 +++++++++++++++++++ 6 files changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb index 712519a60c..96e332c757 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb index 182905c4bb..a29279c43f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb index 8b047bb737..790acc6037 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb index 551c06ecef..0e7eed5918 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb index 2c2c674d2c..8f02974208 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb @@ -29,6 +29,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch new file mode 100644 index 0000000000..39e34a937a --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch @@ -0,0 +1,26 @@ +ensure that Tcl/Tk library paths are correct, to fix segmentation fault that occurs when plotting because system +libraries are picked up; +the problem is that the query_tcktl method guesses the Tk library path based on the Tcl library path by simply +replacing 'Tcl'/'tcl' with 'Tk'/'tk', which doesn't work if the Tk install prefix is different (e.g. due to a +versionsuffix) +author: Kenneth Hoste (HPC-UGent) +-- matplotlib-1.5.1.orig/setupext.py 2016-01-11 04:06:08.000000000 +0100 ++++ matplotlib-1.5.1/setupext.py 2016-04-29 15:43:21.280170000 +0200 +@@ -1560,7 +1560,16 @@ + + # Query Tcl/Tk system for library paths and version string + try: +- tcl_lib_dir, tk_lib_dir, tk_ver = self.query_tcltk() ++ tcl_lib_dir, tk_lib_dir, tk_ver = None, None, None ++ if 'EBROOTTCL' in os.environ and 'EBVERSIONTCL' in os.environ: ++ tcl_ver = '.'.join(os.environ['EBVERSIONTCL'].split('.')[:2]) ++ tcl_lib_dir = os.path.join(os.environ['EBROOTTCL'], 'lib', 'tcl%s' % tcl_ver) ++ if 'EBROOTTK' in os.environ and 'EBVERSIONTK' in os.environ: ++ tk_ver = '.'.join(os.environ['EBVERSIONTK'].split('.')[:2]) ++ tk_lib_dir = os.path.join(os.environ['EBROOTTK'], 'lib', 'tk%s' % tk_ver) ++ ++ if tcl_lib_dir is None or tk_lib_dir is None or tk_ver is None: ++ tcl_lib_dir, tk_lib_dir, tk_ver = self.query_tcltk() + except: + tk_ver = '' + result = self.hardcoded_tcl_config() -- GitLab From a2850e36d1656a502b69931419974015537c8ab3 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 29 Apr 2016 10:08:49 -0400 Subject: [PATCH 607/722] add GTS easyconfig and improve PyGTS easyconfig --- .../easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb | 25 +++++++++++++++++++ .../PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 1 - 2 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb new file mode 100644 index 0000000000..6e89234d6b --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.47.5'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb index d74951a2d3..9d7551949d 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -18,7 +18,6 @@ dependencies = [ ('Python', '2.7.11'), ('GLib', '2.47.5'), ('GTS' ,'0.7.6'), - ('numpy', '1.8.2', versionsuffix), ] options = {'modulename': 'gts'} -- GitLab From be83e907e89d1d3ac81cc14416412fb4ee9f9c58 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:23:05 +0200 Subject: [PATCH 608/722] add easyconfig MPFR-3.1.4-intel-2016a.eb --- .../m/MPFR/MPFR-3.1.4-intel-2016a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb new file mode 100644 index 0000000000..6101f2969d --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.0')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 3cd38ae9e6ddbf1c0541b9aab0c608dc4976e654 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:23:26 +0200 Subject: [PATCH 609/722] add easyconfig GLib-2.48.0-intel-2016a.eb, add easyconfig gettext-0.19.7-intel-2016a.eb --- .../g/GLib/GLib-2.48.0-intel-2016a.eb | 33 +++++++++++++++++++ .../g/gettext/gettext-0.19.7-intel-2016a.eb | 22 +++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb new file mode 100644 index 0000000000..6f5acf6419 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.48.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb new file mode 100644 index 0000000000..d256bae534 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' -- GitLab From b9b61a1d3edfbc23b79c5c001ee8a03bf8e584cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:26:30 +0200 Subject: [PATCH 610/722] add easyconfig Mesa-11.2.1-intel-2016a.eb, modify easyconfig freetype-2.6.3-intel-2016a.eb, add easyconfig pkg-config-0.29.1-intel-2016a.eb, add easyconfig libdrm-2.4.68-intel-2016a.eb, add easyconfig libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb --- ...bXfont-1.5.1-intel-2016a-freetype-2.6.3.eb | 34 ++++++++++ .../l/libdrm/libdrm-2.4.68-intel-2016a.eb | 28 ++++++++ .../m/Mesa/Mesa-11.2.1-intel-2016a.eb | 68 +++++++++++++++++++ .../pkg-config-0.29.1-intel-2016a.eb | 27 ++++++++ 4 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb new file mode 100644 index 0000000000..45a31bc1bd --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +freetype_ver = '2.6.3' +versionsuffix = '-freetype-%s' % freetype_ver + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', freetype_ver), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb new file mode 100644 index 0000000000..e64ac66c51 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.68' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb new file mode 100644 index 0000000000..54f7d8a513 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.2.1' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.68'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1', '-freetype-2.6.3'), + ('LLVM', '3.8.0'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb new file mode 100644 index 0000000000..eeb50eabb1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From eadd15710a076003297e0f6a504471fb0352c211 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:37:23 +0200 Subject: [PATCH 611/722] add easyconfig xcb-util-0.4.0-intel-2016a.eb, add easyconfig xcb-util-image-0.4.0-intel-2016a.eb, add easyconfig xcb-util-keysyms-0.4.0-intel-2016a.eb, add easyconfig xcb-util-renderutil-0.3.9-intel-2016a.eb, add easyconfig xcb-util-wm-0.4.1-intel-2016a.eb --- .../xcb-util-image-0.4.0-intel-2016a.eb | 23 ++++++++++++++++++ .../xcb-util-keysyms-0.4.0-intel-2016a.eb | 24 +++++++++++++++++++ .../xcb-util-renderutil-0.3.9-intel-2016a.eb | 23 ++++++++++++++++++ .../xcb-util-wm-0.4.1-intel-2016a.eb | 23 ++++++++++++++++++ .../x/xcb-util/xcb-util-0.4.0-intel-2016a.eb | 24 +++++++++++++++++++ 5 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb new file mode 100644 index 0000000000..a0cf9f13dd --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-image' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-image package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('xcb-util', '0.4.0'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-image.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb new file mode 100644 index 0000000000..ab965a9d36 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-keysyms' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-keysyms package contains a library for + handling standard X key constants and conversion to/from keycodes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-keysyms.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb new file mode 100644 index 0000000000..c926c17dd1 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-renderutil' +version = '0.3.9' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-renderutil package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-render-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb new file mode 100644 index 0000000000..5d58f2a9b2 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-wm' +version = '0.4.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-%s.so' % x for x in ['ewmh', 'icccm']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb new file mode 100644 index 0000000000..18a587a56e --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util package provides additional extensions to the XCB library, + many that were previously found in Xlib, but are not part of core X protocol""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 5a09c330918abdab2e6129d2c9767a6a29b3b704 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:37:45 +0200 Subject: [PATCH 612/722] add easyconfig fontconfig-2.11.95-intel-2016a.eb, add easyconfig expat-2.1.1-intel-2016a.eb, modify easyconfig freetype-2.6.3-intel-2016a.eb --- .../e/expat/expat-2.1.1-intel-2016a.eb | 16 ++++++++++++++ .../fontconfig-2.11.95-intel-2016a.eb | 22 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb new file mode 100644 index 0000000000..a442e3de7f --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.1' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb new file mode 100644 index 0000000000..09b5a49088 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.95' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.1'), + ('freetype', '2.6.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' -- GitLab From 88739b6f181046a73e49da989652c1cd433c6d9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:42:32 +0200 Subject: [PATCH 613/722] add easyconfig Qt5-5.6.0-intel-2016a.eb, add easyconfig libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb, add easyconfig libxkbcommon-0.6.1-intel-2016a.eb, add easyconfig XKeyboardConfig-2.17-intel-2016a.eb, add easyconfig libxslt-1.1.28-intel-2016a.eb --- .../libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb | 27 +++++++++++++ .../libxkbcommon-0.6.1-intel-2016a.eb | 32 +++++++++++++++ .../l/libxslt/libxslt-1.1.28-intel-2016a.eb | 24 ++++++++++++ .../q/Qt5/Qt5-5.6.0-intel-2016a.eb | 39 +++++++++++++++++++ .../XKeyboardConfig-2.17-intel-2016a.eb | 36 +++++++++++++++++ 5 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..fe3cfb14d6 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesaver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesaver + +dependencies = [ + ('Mesa', mesaver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb new file mode 100644 index 0000000000..8611f0332b --- /dev/null +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxkbcommon' +version = '0.6.1' + +homepage = 'http://xkbcommon.org/' +description = """xkbcommon is a library to handle keyboard descriptions, + including loading them from disk, parsing them and handling their state. + It's mainly meant for client toolkits, window systems, + and other system applications.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xkbcommon.org/download/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libxcb', '1.11.1'), + ('XKeyboardConfig', '2.17'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': ['lib/libxkbcommon%s.so' % x for x in ['', '-x11']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb new file mode 100644 index 0000000000..b3d064b443 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb new file mode 100644 index 0000000000..f4f0ab35bd --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.6.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +dependencies = [ + ('GLib', '2.48.0'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXi', '1.7.6'), + ('xcb-util', '0.4.0'), + ('xcb-util-image', '0.4.0'), + ('xcb-util-keysyms', '0.4.0'), + ('xcb-util-renderutil', '0.3.9'), + ('xcb-util-wm', '0.4.1'), + ('libxkbcommon', '0.6.1'), + ('libXrender', '0.9.9'), + ('fontconfig', '2.11.95'), + ('freetype', '2.6.3'), + ('libXfixes', '5.0.1'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('libXrandr', '1.5.0'), + ('libpng', '1.6.21'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb new file mode 100644 index 0000000000..e72178d939 --- /dev/null +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'XKeyboardConfig' +version = '2.17' + +homepage = 'http://www.freedesktop.org/wiki/Software/XKeyboardConfig/' +description = """The non-arch keyboard configuration database for X Window. + The goal is to provide the consistent, well-structured, + frequently released open source of X keyboard configuration data + for X Window System implementations (free, open source and commercial). + The project is targeted to XKB-based systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.x.org/pub/individual/data/xkeyboard-config/'] +sources = ['xkeyboard-config-%(version)s.tar.bz2'] + +builddependencies = [ + ('libxslt', '1.1.28'), + ('gettext', '0.19.7'), + ('intltool', '0.51.0', '-Perl-5.22.1'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +# see http://www.linuxfromscratch.org/blfs/view/svn/x/xkeyboard-config.html +configopts = '--with-xkb-rules-symlink=xorg ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/X11/xkb'] +} + +moduleclass = 'devel' -- GitLab From d6ed5a22d8156e7fec24f3a3865afa0cb59ba4c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:44:07 +0200 Subject: [PATCH 614/722] bump to CGAL 4.8 using Mesa 11.2.1 as dependency --- ...1.eb => CGAL-4.8-intel-2016a-Python-2.7.11.eb} | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/c/CGAL/{CGAL-4.7-intel-2016a-Python-2.7.11.eb => CGAL-4.8-intel-2016a-Python-2.7.11.eb} (76%) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb similarity index 76% rename from easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb index 1e7bf4a653..fd4219e206 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb @@ -1,5 +1,5 @@ name = 'CGAL' -version = '4.7' +version = '4.8' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.cgal.org/' @@ -12,17 +12,14 @@ toolchainopts = {'strict': True} # note: source URL needs to be updated for a new version (checksums too)! source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] sources = [SOURCE_TAR_XZ] -checksums = ['623d91fb2ab0a35049dc6098a0f235cc'] +checksums = ['e31e7039b5cdc74ac7b106db8ba644f3'] - -mesaver = '11.1.2' dependencies = [ ('Python', '2.7.11'), ('Boost', '1.60.0', versionsuffix), - ('MPFR', '3.1.3', '-GMP-6.1.0'), - ('Qt5', '5.5.1', '-Mesa-%s' % mesaver), - ('Mesa', mesaver, versionsuffix), - ('libGLU', '9.0.0', '-Mesa-%s' % mesaver), + ('MPFR', '3.1.4'), + ('Qt5', '5.6.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " @@ -30,7 +27,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT builddependencies = [ - ('CMake', '3.4.1'), + ('CMake', '3.5.2'), ] moduleclass = 'numlib' -- GitLab From 7c81af64d32804f56413cc5416b97fb2677def34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 23:49:31 +0200 Subject: [PATCH 615/722] modify easyconfig expat-2.1.1-intel-2016a.eb --- easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb index a442e3de7f..6e5b60c35f 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb @@ -10,7 +10,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCELOWER_TAR_BZ2] source_urls = [SOURCEFORGE_SOURCE] moduleclass = 'tools' -- GitLab From 122f7ad45fc9a1a435d6d64345cc2b05dbbf397e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 00:00:08 +0200 Subject: [PATCH 616/722] add missing ncurses dep + --with-libxml2-prefix to gettext easyconfigs --- easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb index d256bae534..4f86721ed0 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb @@ -15,6 +15,7 @@ source_urls = [GNU_SOURCE] dependencies = [ ('libxml2', '2.9.3'), + ('ncurses', '6.0'), ] configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' -- GitLab From 58f5d1437754085e98623da578ab3b58ad86bb29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 00:01:41 +0200 Subject: [PATCH 617/722] add missing ncurses dep + --with-libxml2-prefix to gettext easyconfigs --- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb index b35aee8501..690872c686 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb @@ -18,6 +18,6 @@ dependencies = [ ('ncurses', '5.9'), ] -configopts = '--without-emacs' +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb index 168b2490e6..4580e48c6a 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -18,6 +18,6 @@ dependencies = [ ('ncurses', '6.0'), ] -configopts = '--without-emacs' +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' moduleclass = 'vis' -- GitLab From e069726a05c66e508bbf5651d5a5f935e2856f8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 00:45:06 +0200 Subject: [PATCH 618/722] modify easyconfig GLib-2.48.0-intel-2016a.eb --- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index 6f5acf6419..d241317450 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -21,7 +21,9 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" + +parallel = 1 postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] -- GitLab From 98217a3d259ea96af0512a3970fac83d2d6621d7 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 29 Apr 2016 21:11:40 -0400 Subject: [PATCH 619/722] add GL2PS-1.3.9_foss2016a-mesa11.2.1 --- .../c/CMake/CMake-3.5.2-foss-2016a.eb | 31 +++++++++ .../freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb | 40 +++++++++++ .../f/freetype/freetype-2.6.3-foss-2016a.eb | 22 ++++++ .../GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb | 37 ++++++++++ .../l/LLVM/LLVM-3.8.0-foss-2016a.eb | 41 +++++++++++ .../libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb | 27 ++++++++ ...ibXfont-1.5.1-foss-2016a-freetype-2.6.3.eb | 34 ++++++++++ .../l/libdrm/libdrm-2.4.68-foss-2016a.eb | 28 ++++++++ .../m/Mesa/Mesa-11.2.1-foss-2016a.eb | 68 +++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb | 21 ++++++ .../pkg-config-0.29.1-foss-2016a.eb | 27 ++++++++ 11 files changed, 376 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb new file mode 100644 index 0000000000..9075c094fb --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..1965349120 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', mesa_ver), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb new file mode 100644 index 0000000000..bc610c637e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.3' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..726a6db2a2 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', mesa_ver), + ('libGLU', '9.0.0', versionsuffix), + ('freeglut', '3.0.0', versionsuffix), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb new file mode 100644 index 0000000000..fc0af540c1 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Python', '2.7.11'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..38c8310594 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('Mesa', mesa_ver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb new file mode 100644 index 0000000000..63d5bbf444 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +freetype_ver = '2.6.3' +versionsuffix = '-freetype-%s' % freetype_ver + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', freetype_ver), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb new file mode 100644 index 0000000000..68f8a6be89 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.68' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb new file mode 100644 index 0000000000..a919f2eab9 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.2.1' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.68'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1', '-freetype-2.6.3'), + ('LLVM', '3.8.0'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb new file mode 100644 index 0000000000..a5aab91ad9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1s' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-1.0.1q_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb new file mode 100644 index 0000000000..bb2fea6cae --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 8763ec11daf42708cb05942de98f37dc6f1547fb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 30 Apr 2016 08:51:13 +0100 Subject: [PATCH 620/722] add easyconfig kallisto-0.42.5-foss-2016a.eb --- .../k/kallisto/kallisto-0.42.5-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb new file mode 100644 index 0000000000..2287c59cc6 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.42.5' + +homepage = 'http://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/pachterlab/kallisto/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.4.3')] +dependencies = [('HDF5', '1.8.16', '-serial')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e9a1f252c40bda55d59d7f28cf83b4bbefed3088 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 10:19:47 +0200 Subject: [PATCH 621/722] no need to disable parallel building of GLib --- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index d241317450..918c5aec06 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -23,8 +23,6 @@ builddependencies = [('Python', '2.7.11')] configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" -parallel = 1 - postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] sanity_check_paths = { -- GitLab From a953b7c3339cf33506e33cdbaa31854adcc17ecc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 30 Apr 2016 15:25:19 +0200 Subject: [PATCH 622/722] modify easyconfig makedepend-1.0.5-foss-2016a.eb --- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index 863911703e..3ab1f8aa60 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = [XORG_UTIL_SOURCE] +source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] + +builddependencies = [ + ('xproto', '7.0.28'), +] sanity_check_paths = { 'files': ['bin/makedepend'], -- GitLab From e169054960d7fe14c56efbe8ab31848b0834a460 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 1 May 2016 00:15:18 +0100 Subject: [PATCH 623/722] add easyconfig SCons-2.4.1-foss-2016a-Python-2.7.11.eb --- .../SCons-2.4.1-foss-2016a-Python-2.7.11.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..35083b9098 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' -- GitLab From aa31d54e3c255b37ae53239a86b93ae09956e6ec Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 1 May 2016 00:17:18 +0100 Subject: [PATCH 624/722] add easyconfig Rosetta-2016.13.58602-foss-2016a.eb --- .../Rosetta-2016.13.58602-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb new file mode 100644 index 0000000000..86250d9275 --- /dev/null +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb @@ -0,0 +1,20 @@ +name = 'Rosetta' +version = '2016.13.58602' + +homepage = 'https://www.rosettacommons.org' +description = """Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, +multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and +nucleic acids.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] + +builddependencies = [('SCons', '2.4.1', '-Python-2.7.11')] + +modextravars = { + 'ROSETTA3_DB': '$root/database', +} + +moduleclass = 'bio' -- GitLab From 6c0806d4dee7561c9a7465275e9be2dfdee26d7a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:37:57 +0200 Subject: [PATCH 625/722] modify easyconfig makedepend-1.0.5-foss-2016a.eb --- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index 3ab1f8aa60..c9e59044e7 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +#source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] builddependencies = [ ('xproto', '7.0.28'), -- GitLab From f50236ed9bf05c28dfe03514332307491b0550a9 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:39:37 +0200 Subject: [PATCH 626/722] modify easyconfig makedepend-1.0.5-foss-2016a.eb --- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index c9e59044e7..c4a3658b9f 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -#source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] source_urls = [XORG_UTIL_SOURCE] builddependencies = [ -- GitLab From 1ceb9f59820d3cce159fb76b4c12175c99c2169b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:43:30 +0200 Subject: [PATCH 627/722] modify easyconfig Doxygen-1.8.11-foss-2016a.eb --- easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb index fea350b755..45e774b0e3 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' -- GitLab From f05b80bccdb74af88f109105f8f5423d0f50f6c1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:47:00 +0200 Subject: [PATCH 628/722] modify easyconfig Perl-5.22.1-foss-2016a.eb --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb index 404b98df7e..f1ad7853f0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -137,7 +137,7 @@ exts_list = [ }), ('FreezeThaw', '0.5001', { 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], }), ('DBI', '1.634', { 'source_tmpl': 'DBI-1.634.tar.gz', @@ -221,7 +221,7 @@ exts_list = [ }), ('Tie::Function', '0.02', { 'source_tmpl': 'Tie-Function-0.02.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], }), ('Template::Plugin::Number::Format', '1.06', { 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', -- GitLab From 53c9b1c80a460c6543bbef815d616a396917d8fe Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:57:16 +0200 Subject: [PATCH 629/722] add easyconfig PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- ...-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb new file mode 100644 index 0000000000..0d3d65891c --- /dev/null +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'PLplot' +version = '5.11.1' + +homepage = 'http://plplot.sourceforge.net' +description = """PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols + and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +pyver = '2.7.11' +javaver = '1.7.0_79' +pyshortver = '.'.join(pyver.split('.')[0:2]) +versionsuffix = '-Java-%s-Python-%s' % (javaver, pyver) + +glibver = '2.47.5' + +builddependencies = [ + ('CMake', '3.4.3'), + ('SWIG', '3.0.8', '-foss-2016a-Python-%s' % pyver, True), + ('xproto', '7.0.28'), +] + +dependencies = [ + ('Java', javaver, '', True), + ('Python', pyver), + ('Perl', '5.22.1'), + ('Tcl', '8.6.4'), + ('Tk', '8.6.4', '-no-X11'), + ('cairo', '1.14.6'), + ('expat', '2.1.0'), + ('fontconfig', '2.11.94'), + ('freetype', '2.6.2'), + ('GLib', glibver), + ('libICE', '1.0.9'), + ('libtool', '2.4.6'), + ('libX11', '1.6.3'), + ('libXau', '1.0.8'), + ('libxcb', '1.11.1'), + ('libXdmcp', '1.1.2'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), + ('Pango', '1.39.0'), + ('pixman', '0.34.0'), + ('zlib', '1.2.8') +] + +separate_build_dir = True + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': ['lib/libplplot.so', 'lib/pkgconfig/plplot-f95.pc'], + 'dirs': ['bin', 'include/plplot', 'lib/fortran/modules/plplot', 'lib/pkgconfig', 'share/man/man1'], +} + +moduleclass = 'vis' -- GitLab From 44b6590f2ca4b0683e2a2b922ebec71d555f0e25 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 15:50:56 +0200 Subject: [PATCH 630/722] builddep up --- .../easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb index 444de341bf..2facea57d9 100644 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb @@ -19,12 +19,13 @@ sources = ['%(name)s_%(version)s.tgz'] dependencies = [('Boost', '1.60.0')] +builddependencies = [('CMake', '3.4.3',)] + + start_dir = 'src' configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" -builddependencies = [('CMake', '3.4.3',)] - sanity_check_paths = { 'files': ['bin/CrossTalkZ'], 'dirs': [''], -- GitLab From d5f98a30a0c96ca87d29c8b47200cb2c4d6450a5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 16:08:28 +0200 Subject: [PATCH 631/722] version fix, commit version provided --- ....eb => Commet-20150415-foss-2016a-Python-2.7.11.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/c/Commet/{Commet-20160422-foss-2016a-Python-2.7.11.eb => Commet-20150415-foss-2016a-Python-2.7.11.eb} (76%) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb similarity index 76% rename from easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 2c16bccce7..88a548fab4 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -1,7 +1,8 @@ easyblock = 'MakeCp' name = 'Commet' -version = '20160422' +version = '20150415' +commit = '4ef0705' pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' @@ -13,11 +14,10 @@ a large metagenomic project. toolchain = {'name': 'foss', 'version': '2016a'} -# there is no tarball provided, only git checkout through: -# https://github.com/pierrepeterlongo/commet/archive/master.zip -sources = [SOURCE_ZIP] +source_urls = ['https://github.com/pierrepeterlongo/commet/archive'] +sources = ['%s.tar.gz' % commit] -checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] +checksums = ['19cba09ca7a92eaed75ed6af820d9451'] files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] -- GitLab From 540113e091905d193da3fcdc0c803424c34acd4a Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 17:24:15 +0200 Subject: [PATCH 632/722] Exonerate with foss2016a --- .../e/Exonerate/Exonerate-2.4.0-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb new file mode 100644 index 0000000000..0cfe11f239 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'http://www.ebi.ac.uk/~guy/exonerate/' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/nathanweeks/exonerate/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GLib', '2.47.5')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' -- GitLab From 01bc3c39e0364364ea288d9e64c6adacf4533d63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 1 May 2016 18:54:55 +0200 Subject: [PATCH 633/722] also add xproto as build dep in other makedepend 1.0.5 easyconfigs --- .../makedepend-1.0.5-gimkl-2.11.5.eb | 4 ++++ .../makedepend-1.0.5-intel-2015a.eb | 4 ++++ .../makedepend-1.0.5-intel-2015b.eb | 4 ++++ .../makedepend-1.0.5-intel-2016a.eb | 4 ++++ .../x/xproto/xproto-7.0.28-intel-2015a.eb | 24 +++++++++++++++++++ 5 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb index 38d76d37d2..29139d3313 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb index 282179280a..2a137852f4 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb index ca6025105b..32cc5814c9 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb index e38d07d26e..943da96f82 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb new file mode 100644 index 0000000000..532a92d315 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 4a496d0696387804d39ae0782243921dcc9a5006 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 21:45:01 +0200 Subject: [PATCH 634/722] Style fixes --- .../Commet-20150415-foss-2016a-Python-2.7.11.eb | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 88a548fab4..6c4d59ab68 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -3,13 +3,11 @@ easyblock = 'MakeCp' name = 'Commet' version = '20150415' commit = '4ef0705' - -pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' homepage = 'https://colibread.inria.fr/software/commet/' description = """ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of -a large metagenomic project. + a large metagenomic project. """ toolchain = {'name': 'foss', 'version': '2016a'} @@ -19,15 +17,15 @@ sources = ['%s.tar.gz' % commit] checksums = ['19cba09ca7a92eaed75ed6af820d9451'] -files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] - dependencies = [ ('Python', '2.7.11'), ] +files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] + sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["Commet.py", "bvop", - "compare_reads", "extract_reads", "filter_reads", "index_and_search"]], + 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', + 'extract_reads', 'filter_reads', 'index_and_search']], 'dirs' : ['doc', 'include'] } -- GitLab From 9e74175aa5e6096dcc34ad1f3a502b9a84dcfecc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 08:42:42 +0200 Subject: [PATCH 635/722] Add SWIG-3.0.8-foss-2016a-Python-2.7.11.eb --- .../SWIG-3.0.8-foss-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..2ffde034da --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '3.0.8' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.11' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' -- GitLab From 7c7e981088c0df6a663f3ad8626980db936c01b3 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 08:49:05 +0200 Subject: [PATCH 636/722] Modify Perl-5.22.1-intel-2016a.eb to update source_urls --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index aed8a467d0..b58ce50af4 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -137,7 +137,7 @@ exts_list = [ }), ('FreezeThaw', '0.5001', { 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], }), ('DBI', '1.634', { 'source_tmpl': 'DBI-1.634.tar.gz', @@ -221,7 +221,7 @@ exts_list = [ }), ('Tie::Function', '0.02', { 'source_tmpl': 'Tie-Function-0.02.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], }), ('Template::Plugin::Number::Format', '1.06', { 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', -- GitLab From 1d32aabaede918e266733560e3c7e573cd63b066 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 09:00:15 +0200 Subject: [PATCH 637/722] Modify Doxygen-1.8.11-* files to only build in serial --- easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb | 2 ++ easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb | 2 ++ easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb index 5adccf48d7..9af65e4593 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb index 1db648e43d..5b5d5f06cd 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb index 2d5dc8597f..a63ff80fea 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' -- GitLab From 752eeed94e82927ba6a1e12b2966bd95cd1a0342 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 10:07:56 +0200 Subject: [PATCH 638/722] bump Java to 1.7.0_80, use %(pyver)s, %(javaver)s templates --- ...-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb} | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/p/PLplot/{PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb => PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb} (77%) diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb similarity index 77% rename from easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb rename to easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb index 0d3d65891c..a77bf58f49 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'CMakeMake' name = 'PLplot' version = '5.11.1' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' homepage = 'http://plplot.sourceforge.net' description = """PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols @@ -13,22 +14,15 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -pyver = '2.7.11' -javaver = '1.7.0_79' -pyshortver = '.'.join(pyver.split('.')[0:2]) -versionsuffix = '-Java-%s-Python-%s' % (javaver, pyver) - -glibver = '2.47.5' - builddependencies = [ ('CMake', '3.4.3'), - ('SWIG', '3.0.8', '-foss-2016a-Python-%s' % pyver, True), + ('SWIG', '3.0.8', '-Python-%(pyver)s'), ('xproto', '7.0.28'), ] dependencies = [ - ('Java', javaver, '', True), - ('Python', pyver), + ('Java', '1.7.0_80', '', True), + ('Python', '2.7.11'), ('Perl', '5.22.1'), ('Tcl', '8.6.4'), ('Tk', '8.6.4', '-no-X11'), @@ -36,7 +30,7 @@ dependencies = [ ('expat', '2.1.0'), ('fontconfig', '2.11.94'), ('freetype', '2.6.2'), - ('GLib', glibver), + ('GLib', '2.47.5'), ('libICE', '1.0.9'), ('libtool', '2.4.6'), ('libX11', '1.6.3'), @@ -52,7 +46,7 @@ dependencies = [ separate_build_dir = True -modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_paths = { 'files': ['lib/libplplot.so', 'lib/pkgconfig/plplot-f95.pc'], -- GitLab From 68da87ecb25dc92b328c3c313eaeb8192e6269d2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 10:59:03 +0200 Subject: [PATCH 639/722] add easyconfig SPRNG-2.0b-foss-2016a.eb --- .../s/SPRNG/SPRNG-2.0b-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb new file mode 100644 index 0000000000..59be5269fa --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'SPRNG' +version = '2.0b' + +homepage = 'http://www.sprng.org/' +description = "Scalable Parallel Pseudo Random Number Generators Library" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.sprng.org/Version2.0/'] +sources = ['%(namelower)s%(version)s.tar.gz'] + +patches = ['SPRNG-2.0_fix-metropolis-test.patch'] + +dependencies = [('GMP', '6.1.0')] + +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' + +# does not support parallel build +parallel = 1 + +files_to_copy = [ + (['lib/libsprng.a'], 'lib'), + (['include/interface.h', 'include/sprng.h', 'include/sprng_f.h'], 'include'), +] + +sanity_check_paths = { + 'files': ["lib/libsprng.a"], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From f12417d1caa6603e778b58af79d1235ad42d74db Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 2 May 2016 11:53:18 +0200 Subject: [PATCH 640/722] removed tab --- .../c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 6c4d59ab68..549296f08e 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -25,7 +25,7 @@ files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', - 'extract_reads', 'filter_reads', 'index_and_search']], + 'extract_reads', 'filter_reads', 'index_and_search']], 'dirs' : ['doc', 'include'] } -- GitLab From d9ccb6471e949227ec1acd518aa95cf819737b81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 11:56:40 +0200 Subject: [PATCH 641/722] add easyconfig TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb, add easyconfig molmod-1.1-intel-2016a-Python-2.7.11.eb --- .../molmod-1.1-intel-2016a-Python-2.7.11.eb | 31 ++++++++++++++++++ .../TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb | 32 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1673c64e60 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), +] + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" + +# fix permissions issue on files in share/molmod subdir +postinstallcmds = ['chmod -R o+r %(installdir)s/share/molmod'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/molmod'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..34a9b5e9f5 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'TAMkin' +version = '1.0.9' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), + ('molmod', '1.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'chem' -- GitLab From 7e1df6e4e780696abbb408d269a01c77f473ee82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 12:10:49 +0200 Subject: [PATCH 642/722] add easyconfig FFmpeg-2.8.7-intel-2016a.eb --- .../f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb new file mode 100644 index 0000000000..05478ccada --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.7' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('x264', '20160430'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From 56d851d169447389e2ee3cdfd4b04ef3e6f12a8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 12:55:35 +0200 Subject: [PATCH 643/722] add easyconfig GTK+-2.24.30-intel-2016a.eb, add easyconfig Pango-1.40.1-intel-2016a.eb, add easyconfig cairo-1.14.6-intel-2016a-GLib-2.48.0.eb, add easyconfig HarfBuzz-1.2.7-intel-2016a.eb, add easyconfig ATK-2.20.0-intel-2016a.eb, add easyconfig Gdk-Pixbuf-2.35.1-intel-2016a.eb, add easyconfig GObject-Introspection-1.48.0-intel-2016a.eb --- .../a/ATK/ATK-2.20.0-intel-2016a.eb | 34 +++++++++++ .../cairo-1.14.6-intel-2016a-GLib-2.48.0.eb | 56 +++++++++++++++++++ ...Object-Introspection-1.48.0-intel-2016a.eb | 48 ++++++++++++++++ .../g/GTK+/GTK+-2.24.30-intel-2016a.eb | 25 +++++++++ .../Gdk-Pixbuf-2.35.1-intel-2016a.eb | 34 +++++++++++ .../h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb | 34 +++++++++++ .../p/Pango/Pango-1.40.1-intel-2016a.eb | 31 ++++++++++ 7 files changed, 262 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb new file mode 100644 index 0000000000..2c8911864b --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.20.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000..ecd56f9166 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' +glibver = '2.48.0' +versionsuffix = '-GLib-%s' % glibver + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.3'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.95'), + ('expat', '2.1.1'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] +builddependencies = [ + ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb new file mode 100644 index 0000000000..3d59c6fe7c --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.48.0' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('Python', '2.7.11'), + ('GLib', glibver), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6', '-GLib-%s' % glibver), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb new file mode 100644 index 0000000000..6dfeab0526 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.30' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.20.0'), + ('Gdk-Pixbuf', '2.35.1'), + ('Pango', '1.40.1'), + ('GObject-Introspection', '1.48.0'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb new file mode 100644 index 0000000000..f06da781d8 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.35.1' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb new file mode 100644 index 0000000000..23c2924fab --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.2.7' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('freetype', '2.6.3'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb new file mode 100644 index 0000000000..b251f8ef22 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.1' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('HarfBuzz', '1.2.7'), + ('GObject-Introspection', '1.48.0'), + ('fontconfig', '2.11.95') +] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From b430a93dab623ccdbb1cbab087ef880ceac1942c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 13:12:56 +0200 Subject: [PATCH 644/722] add easyconfig NASM-2.12.01-intel-2016a.eb, add easyconfig x264-20160430-intel-2016a.eb --- .../n/NASM/NASM-2.12.01-intel-2016a.eb | 31 +++++++++++++++++++ .../x/x264/x264-20160430-intel-2016a.eb | 24 ++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb new file mode 100644 index 0000000000..dc884fc260 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.01' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb new file mode 100644 index 0000000000..2525aff2b3 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160430' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://ftp.videolan.org/pub/videolan/x264/snapshots/'] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From a4e13eba05271a1af27d9e133bab189308dfe211 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 13:48:06 +0200 Subject: [PATCH 645/722] modify easyconfig x264-20160430-intel-2016a.eb --- easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb index 2525aff2b3..5f7b69a6bc 100644 --- a/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb +++ b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb @@ -9,7 +9,10 @@ description = """x264 is a free software library and application for encoding vi toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['ftp://ftp.videolan.org/pub/videolan/x264/snapshots/'] +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] dependencies = [('Yasm', '1.3.0')] -- GitLab From e98a77f0534b917a23df6f63b4f7975391815725 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 15:09:25 +0200 Subject: [PATCH 646/722] add easyconfig OpenCV-2.4.12-intel-2016a.eb --- .../o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb new file mode 100644 index 0000000000..5cbe53aac8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -0,0 +1,69 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '2.4.12' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_ZIP] +source_urls = [('http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/%(version)s', 'download')] + +patches = ['OpenCV-%(version)s_with_IPP.patch'] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +javaver = '1.7.0_80' +dependencies = [ + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('FFmpeg', '2.8.7'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('JasPer', '1.900.1'), + ('Java', javaver, '', True), + ('ant', '1.9.6', '-Java-%s' % javaver, True), + ('GLib', '2.48.0'), + ('GTK+', '2.24.30'), +] + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.so ' +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.so ' +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.so ' +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' -- GitLab From 01c5819ff4a7441070afba2a3d05fc512b2e3e1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 16:37:32 +0200 Subject: [PATCH 647/722] use existing patch file, fix conflict on NASM version --- ...eg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb | 33 +++++++++++++++++++ .../o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 8 ++--- 2 files changed, 37 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb new file mode 100644 index 0000000000..c1f7d100e0 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +nasmver = '2.12.01' +versionsuffix = '-NASM-%s' % nasmver + +dependencies = [ + ('NASM', nasmver), +] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb index 5cbe53aac8..89e2746bd8 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -11,10 +11,10 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCELOWER_ZIP] -source_urls = [('http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/%(version)s', 'download')] +source_urls = ['https://github.com/Itseez/opencv/archive/'] +sources = ['%(version)s.zip'] -patches = ['OpenCV-%(version)s_with_IPP.patch'] +patches = ['OpenCV-2.4.9_with_IPP.patch'] builddependencies = [ ('CMake', '3.5.2'), @@ -25,7 +25,7 @@ dependencies = [ ('Python', '2.7.11'), ('zlib', '1.2.8'), ('FFmpeg', '2.8.7'), - ('libjpeg-turbo', '1.4.2'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), -- GitLab From 1dc2cb9ea6258091ac20deafdd03dc35dfd23bcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 17:05:52 +0200 Subject: [PATCH 648/722] add sed command to worker easyconfig files to fix module_path in conf/worker.conf --- .../easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 9 +++++---- .../easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index cdf0174497..66e66633d0 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -21,11 +21,12 @@ dependencies = [ # adjust worker configuration file # note: tweak this to your local setup postinstallcmds = [ - 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', - 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', # tweak this - 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', # tweak this (maybe) - 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2015a@g" %(installdir)s/conf/worker.conf', # tweak this (maybe) + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb index 3c373e597a..f840fe2253 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb @@ -21,11 +21,12 @@ dependencies = [ # adjust worker configuration file # note: tweak this to your local setup postinstallcmds = [ - 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', - 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', # tweak this - 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', # tweak this (maybe) - 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', # tweak this (maybe) + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' -- GitLab From 674a21915757f47ee9b7847046f3342ea1c5f39a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 17:26:36 +0200 Subject: [PATCH 649/722] add easyconfig FFTW-3.3.4-intel-2016a.eb --- .../f/FFTW/FFTW-3.3.4-intel-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb new file mode 100644 index 0000000000..09d52dd755 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +# no quad precision, requires GCC v4.6 or higher +# see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' -- GitLab From 9c81999977bfae80711d38da02ebd8912caa5468 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 17:32:59 +0200 Subject: [PATCH 650/722] make Gdk-Pixbug 2.35.1 compatible with NASM 2.12.01 --- .../easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb index f06da781d8..ec51681b28 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('GLib', '2.48.0'), - ('libjpeg-turbo', '1.4.2'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('GObject-Introspection', '1.48.0') -- GitLab From 0933f2c4ce3c791af9049d58a213777de638df6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 19:13:57 +0200 Subject: [PATCH 651/722] correct sed command in worker easyconfig files to fix module_path in conf/worker.conf --- easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index 66e66633d0..1bd2831171 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -26,7 +26,7 @@ postinstallcmds = [ 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', - 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb index f840fe2253..1882b094dc 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb @@ -26,7 +26,7 @@ postinstallcmds = [ 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', - 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' -- GitLab From dcd16bf4a00f49d8511d31f894606d306cb5b08e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 19:47:01 +0200 Subject: [PATCH 652/722] bump hwloc to 1.11.3, add missing hwloc easyconfig file --- .../hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb | 22 +++++++++++++++++++ .../OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 2 +- 2 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..54ea46766a --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +# numactl is a direct dependency of PGI +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index 8cd6dea646..be813ed50e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -18,7 +18,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify -dependencies = [('hwloc', '1.11.2')] +dependencies = [('hwloc', '1.11.3')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -- GitLab From ced0e99cf03255aa46d0855c8ee42cfe2e691835 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:18:33 +0200 Subject: [PATCH 653/722] add easyconfig ParaView-4.4.0-intel-2016a.eb --- .../p/ParaView/ParaView-4.4.0-intel-2016a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb new file mode 100644 index 0000000000..5961519cd4 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '4.4.0' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': False} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s-source.tar.gz"] + +patches = ['%(name)s-%(version)s_missingheader.patch'] + +dependencies = [ + ('Mesa', '11.2.1'), + ('libGLU', '9.0.0'), + ('libXt', '1.1.5'), + ('Qt', '4.8.7'), + ('libXext', '1.3.3'), + ('libX11', '1.6.3'), + ('zlib', '1.2.8'), +] + +builddependencies = [('CMake', '3.5.2')] + +separate_build_dir = True + +maxparallel = 4 + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +# Without internet connection turn off testing (uncomment the following line) +#configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From bb3540dfc10e41c0550bb4aa18610f15e8be76f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:23:40 +0200 Subject: [PATCH 654/722] modify easyconfig ParaView-4.4.0-intel-2016a.eb, add easyconfig libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb --- .../libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb | 27 +++++++++++++++++++ .../p/ParaView/ParaView-4.4.0-intel-2016a.eb | 3 +-- 2 files changed, 28 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..fe3cfb14d6 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesaver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesaver + +dependencies = [ + ('Mesa', mesaver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index 5961519cd4..dd7ed0db4e 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -16,8 +16,7 @@ sources = ["ParaView-v%(version)s-source.tar.gz"] patches = ['%(name)s-%(version)s_missingheader.patch'] dependencies = [ - ('Mesa', '11.2.1'), - ('libGLU', '9.0.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), ('libXt', '1.1.5'), ('Qt', '4.8.7'), ('libXext', '1.3.3'), -- GitLab From 4d95db4024048043a88926c1ab85b70103c54b1b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 3 May 2016 11:38:51 +0200 Subject: [PATCH 655/722] LASTZ with foss2016a --- .../l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb new file mode 100644 index 0000000000..6f1e587143 --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'LASTZ' +version = '1.02.00' + +homepage = 'http://www.bx.psu.edu/~rsharris/lastz/' +description = """ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle + sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS + sequencing technologies such as Roche 454. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] + +patches = ['LASTZ-Makefile.patch'] + +skipsteps=['configure'] + +installopts = 'installDir=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["lastz","lastz_D"]], + 'dirs': ["bin"] +} + +moduleclass = 'bio' -- GitLab From bd6a68f0019b2a28271c533b904a43dea7518149 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:50:20 +0200 Subject: [PATCH 656/722] disable testing for ParaView --- easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index dd7ed0db4e..e9e923fc24 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -34,7 +34,7 @@ configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' # Without internet connection turn off testing (uncomment the following line) -#configopts += '-DBUILD_TESTING=OFF ' +configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) -- GitLab From a5acebaa141c7adea90c1ebc41016336c2c231bd Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 3 May 2016 11:53:50 +0200 Subject: [PATCH 657/722] comments exts --- .../BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 1e9c0c19f5..fdb264f023 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -18,12 +18,13 @@ dependencies = [ ('DB_File', '1.835', versionsuffix), ] -exts_list = [ - ('CGI', '4.28', { - 'source_tmpl': 'CGI-4.28.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], - }), -] +#exts_list = [ +# ('CGI', '4.28', { +# 'source_tmpl': 'CGI-4.28.tar.gz', +# 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], +# }), +#] + options = {'modulename': 'Bio::Perl'} moduleclass = 'bio' -- GitLab From 9b8e5bb3f71195e5ada26a6ebfa928b8772a03f7 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 3 May 2016 11:55:27 +0200 Subject: [PATCH 658/722] modify easyconfig Blitz++-0.10-foss-2016a.eb, modify easyconfig Blitz++-0.10-goolf-1.5.16.eb --- easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb | 2 ++ easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb index f91bad5dd3..f5aaed761c 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb @@ -17,4 +17,6 @@ sanity_check_paths = { 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], } +configopts = '--enable-shared' + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb index f75014e6f2..e75ab2de98 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb @@ -17,4 +17,6 @@ sanity_check_paths = { 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], } +configopts = '--enable-shared' + moduleclass = 'lib' -- GitLab From 9d63140391fe52ab6161f2df09171600fa04a875 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:57:35 +0200 Subject: [PATCH 659/722] add easyconfig grace-5.1.25-intel-2016a.eb, add easyconfig util-linux-2.28-intel-2016a.eb, add easyconfig motif-2.3.5-intel-2016a.eb, add easyconfig xbitmaps-1.1.1-intel-2016a.eb --- .../g/grace/grace-5.1.25-intel-2016a.eb | 29 ++++++++++++ .../m/motif/motif-2.3.5-intel-2016a.eb | 47 +++++++++++++++++++ .../util-linux/util-linux-2.28-intel-2016a.eb | 33 +++++++++++++ .../x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb | 19 ++++++++ 4 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb new file mode 100644 index 0000000000..e538b0ca3b --- /dev/null +++ b/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'grace' +version = '5.1.25' + +homepage = 'http://freecode.com/projects/grace' +description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" + +source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('motif', '2.3.5'), + ('netCDF', '4.4.0'), +] + +runtest = 'tests' + +# we also need to run make links right before or after make install. +installopts = 'links' + +sanity_check_paths = { + 'files': ['bin/xmgrace'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb new file mode 100644 index 0000000000..ed700e2d0b --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.5' + +homepage = 'http://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +# use -O1 to dance around icc segfaulting +toolchainopts = {'lowopt': True} + +sources = ['%(name)s-%(version)s-src.tgz'] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('libXt', '1.1.5'), + ('libXau', '1.0.8'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXdmcp', '1.1.2'), + ('libpng', '1.6.21'), + ('xbitmaps', '1.1.1'), + ('freetype', '2.6.3'), + ('libjpeg-turbo', '1.4.2'), + ('bzip2', '1.0.6'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('util-linux', '2.28'), +] + +preconfigopts = "./autogen.sh && " + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb new file mode 100644 index 0000000000..d86cc6a029 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.28' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb new file mode 100644 index 0000000000..a463f1ce79 --- /dev/null +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xbitmaps' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """provides bitmaps for x""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_DATA_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From f574411b83f9fda2f0dda5862b40ae1996aaa6f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 12:04:35 +0200 Subject: [PATCH 660/722] fix source URL for motif 2.3.5 --- easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb index ed700e2d0b..60a8ac80b7 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # use -O1 to dance around icc segfaulting toolchainopts = {'lowopt': True} -sources = ['%(name)s-%(version)s-src.tgz'] +sources = ['%(name)s-%(version)s.tgz'] source_urls = [SOURCEFORGE_SOURCE] dependencies = [ -- GitLab From 16f0c91739daa1cdf1cd19d283b29ae22a246d3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 12:09:34 +0200 Subject: [PATCH 661/722] really fix name of source tarball for motif 2.3.5 --- easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb index 60a8ac80b7..8072aeb7c2 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # use -O1 to dance around icc segfaulting toolchainopts = {'lowopt': True} -sources = ['%(name)s-%(version)s.tgz'] +sources = ['%(name)s-%(version)s.tar.gz'] source_urls = [SOURCEFORGE_SOURCE] dependencies = [ -- GitLab From 025a13b46c76146c6ddcb0c82b80b741c34e09e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 12:18:58 +0200 Subject: [PATCH 662/722] no autogen for motif 2.3.5 --- easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb index 8072aeb7c2..0cf658c9a2 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -34,8 +34,6 @@ builddependencies = [ ('util-linux', '2.28'), ] -preconfigopts = "./autogen.sh && " - # makefile is not parallel safe parallel = 1 -- GitLab From 17fed7291663dfab3144c3c71acbfa5461e73a24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 13:39:08 +0200 Subject: [PATCH 663/722] no need to limit parallel build for ParaView --- easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index e9e923fc24..838808a743 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -28,8 +28,6 @@ builddependencies = [('CMake', '3.5.2')] separate_build_dir = True -maxparallel = 4 - configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' -- GitLab From 596390a3f4ace66c6329792d3e3849d2d45dc4c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 May 2016 13:42:09 +0200 Subject: [PATCH 664/722] clean up binutils 2.26 easyconfigs to use binutils easyblock --- .../b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 20 ------------------- .../easyconfigs/b/binutils/binutils-2.26.eb | 20 ------------------- 2 files changed, 40 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb index ca71c5f04e..d7c829040f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.26' @@ -20,22 +18,4 @@ builddependencies = [ ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb index 5145e1becd..702b413120 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.26' @@ -18,22 +16,4 @@ builddependencies = [ ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' -- GitLab From 8580725e82c0690321e07d4588b0dfdac13968e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 May 2016 14:30:10 +0200 Subject: [PATCH 665/722] clean up binutils easyconfigs to use binutils easyblock --- .../binutils-2.22-goalf-1.1.0-no-OFED.eb | 14 ----------- .../binutils-2.22-gompi-1.4.12-no-OFED.eb | 14 ----------- .../b/binutils/binutils-2.22-goolf-1.4.10.eb | 14 ----------- .../b/binutils/binutils-2.22-goolf-1.5.14.eb | 11 --------- .../b/binutils/binutils-2.24-foss-2014b.eb | 13 ----------- .../b/binutils/binutils-2.24-intel-2014b.eb | 16 ------------- .../binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 23 +------------------ .../binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCC-4.9.3.eb | 23 +------------------ .../binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 22 +----------------- .../easyconfigs/b/binutils/binutils-2.25.1.eb | 22 +----------------- .../easyconfigs/b/binutils/binutils-2.25.eb | 22 +----------------- 15 files changed, 9 insertions(+), 273 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index bfc339020f..af12b0472e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,15 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 437f04c2a6..8035182b62 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,15 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index 5f76d89a06..de87300f7c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -23,15 +20,4 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb index 5dae8ebe27..d989a00acf 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,12 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%(version)s.tar.bz2'] source_urls = [GNU_SOURCE] -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb index 3d49fdcf03..9683cfc728 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.24' @@ -15,15 +13,4 @@ dependencies = [ ('zlib', '1.2.8'), ] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 77fb03962b..5d4b31cd73 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.24' @@ -15,18 +13,4 @@ dependencies = [ ('zlib', '1.2.8'), ] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -# disable warning/error #175 ("subscript out of range") -buildopts = 'CFLAGS="$CFLAGS -wd175"' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index c3ffc6e24a..08e10d150c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 418f81f5f1..ea9a13974b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -11,30 +9,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -# zlib required, but being linked instatically, so not a runtime dep builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 2e680c9ce3..9709696cf5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index b6d6a68fc6..7ccace8501 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -11,30 +9,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -# zlib required, but being linked instatically, so not a runtime dep builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index 6858b124b1..d6e68008e5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb index a9d4815d89..9ec7a3f3f3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,28 +13,10 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 5378940837..f411442d12 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,28 +13,10 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index 63837a712c..e3f5b15724 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25.1' @@ -14,26 +12,8 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index cfcfe38d3d..e08cd975ad 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,26 +13,8 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' -- GitLab From 52e2b45e866b5d6c1c3779d6f19ebba6a3c12aa8 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 10:55:13 -0400 Subject: [PATCH 666/722] bump to GLib 2.48.0 --- .../g/GLib/GLib-2.48.0-foss-2016a.eb | 33 +++++++++++++++++++ .../PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb new file mode 100644 index 0000000000..73ce1be6d6 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.48.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb index 9d7551949d..1438b0e86a 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.11'), - ('GLib', '2.47.5'), + ('GLib', '2.48.0'), ('GTS' ,'0.7.6'), ] -- GitLab From 61d8f74df864995f4a49d53ef64d108cd9ddf585 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 11:14:12 -0400 Subject: [PATCH 667/722] bump to mesa 11.2.1 --- ...bQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..3f7a781e6b --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,23 @@ +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('libGLU', '9.0.0', versionsuffix), +] + +builddependencies = [('Qt', '4.8.7', '-GLib-2.48.0')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' -- GitLab From 16181d207a81520c7b3d0b80143f37fb9a9e181f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 11:23:58 -0400 Subject: [PATCH 668/722] add Qt 4.8.7 with GLib-2.48.0 --- .../q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000..8616257c5c --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb @@ -0,0 +1,27 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +glib_ver = '2.48.0' +versionsuffix = '-GLib-%s' % glib_ver + +dependencies = [ + ('GLib', glib_ver), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXrender', '0.9.9'), +] + +moduleclass = 'devel' -- GitLab From c3b8ffb5250bcdba45838b4b54b402414f6d9697 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 11:53:26 -0400 Subject: [PATCH 669/722] bump to GLib 2.48.0 --- easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb index 6e89234d6b..cca1bedcdd 100644 --- a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb @@ -14,7 +14,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('GLib', '2.47.5'), + ('GLib', '2.48.0'), ] sanity_check_paths = { -- GitLab From 8fc70c4034eaa8b0c805a15fa4cd50daf5fafa8e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:17:17 +0200 Subject: [PATCH 670/722] provided patch --- .../easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 2 +- .../easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch | 12 ++++++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb index 6f1e587143..e032219f9e 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] -patches = ['LASTZ-Makefile.patch'] +patches = ['LASTZ-1.02.00_Makefile.patch'] skipsteps=['configure'] diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch new file mode 100644 index 0000000000..e0aa55dbeb --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch @@ -0,0 +1,12 @@ +--- lastz-distrib-1.02.00/src/Makefile 2010-01-13 18:00:09.000000000 +0100 ++++ lastz-distrib-1.02.00/src/Makefile 2015-02-09 17:22:41.030256461 +0100 +@@ -28,7 +28,7 @@ + # + #--------- + +-definedForAll = -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE ++definedForAll = -Wall -Wextra -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE + + + VERSION_FLAGS= \ + -- GitLab From a2668ad34eeac9de4a4f5cb2e78272e9dd042329 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:20:41 +0200 Subject: [PATCH 671/722] quickfixes --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb index e032219f9e..76b32edded 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -16,12 +16,12 @@ source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] patches = ['LASTZ-1.02.00_Makefile.patch'] -skipsteps=['configure'] +skipsteps = ['configure'] installopts = 'installDir=%(installdir)s/bin' sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["lastz","lastz_D"]], + 'files': ["bin/%s" % binfile for binfile in ["lastz", "lastz_D"]], 'dirs': ["bin"] } -- GitLab From 1930b858c49360948b786786cbb6aeffc4e17d96 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:47:49 +0200 Subject: [PATCH 672/722] FFmpeg with foss2016a --- .../f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb new file mode 100644 index 0000000000..b93565bb4f --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.7' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.11.08'), + ('zlib', '1.2.8'), + ('x264', '20160114'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From a29a5c6c3bbe98becf368f5dff527ddf07b413e4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:51:38 +0200 Subject: [PATCH 673/722] FIAT with foss2016a --- .../FIAT-1.6.0-foss-2016a-Python-2.7.11.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..649eb41225 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '1.6.0' + +homepage = 'https://bitbucket.org/fenics-project/fiat' +description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order +instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating +arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +pyver = '2.7.11' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('sympy', '0.7.6.1', versionsuffix), +] + +options = {'modulename': name} + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'math' -- GitLab From 14050d83c1b95894071cb5da2fb4ea2ec1da3158 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 May 2016 14:24:43 +0200 Subject: [PATCH 674/722] disable necessary buildopts for binutils 2.24 w/ intel/2014b --- easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 5d4b31cd73..7598e76c07 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -13,4 +13,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# disable warning/error #175 ("subscript out of range") +buildopts = 'CFLAGS="$CFLAGS -wd175"' + moduleclass = 'tools' -- GitLab From 8292a831911188e5673f608d0de9abc0c81a4ca2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 May 2016 21:12:59 +0200 Subject: [PATCH 675/722] {toolchain}[dummy] intel/2016.03-GCC-5.3 --- .../h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb | 18 ++++++++++ .../i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb | 33 +++++++++++++++++ .../iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 18 ++++++++++ .../ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 33 +++++++++++++++++ .../i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb | 20 +++++++++++ ...11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb | 36 +++++++++++++++++++ ....181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 33 +++++++++++++++++ .../i/intel/intel-2016.03-GCC-5.3.eb | 26 ++++++++++++++ 8 files changed, 217 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb new file mode 100644 index 0000000000..7eaca67c16 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.03-GCC-5.3'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..d81ed4bdf9 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['d6f8529a44231e427219c8e025dec3b2'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..a1f40c75ae --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.3.210' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..703424d3e0 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..8e5a35ceef --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.03' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..82e5a9af1a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-5.3.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..cc0d58235f --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.3.0-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb new file mode 100644 index 0000000000..3de185ca63 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.03' +gcc_maj_min = '5.3' +versionsuffix = '-GCC-%s' % gcc_maj_min + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +gccver = '%s.0' % gcc_maj_min +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' -- GitLab From 09b4e9468c5dd27612574fa2da9448e66dd37a2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 May 2016 07:29:48 +0200 Subject: [PATCH 676/722] fix checksums for icc/ifort 2016.3 and imkl 11.3.3 --- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb index d81ed4bdf9..2192bcc506 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] -checksums = ['d6f8529a44231e427219c8e025dec3b2'] +checksums = ['b256c5573d4bba3692c9c4a6ac994d1c'] gccver = '5.3.0' binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index 703424d3e0..b354753609 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] -checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] +checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] gccver = '5.3.0' binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb index 82e5a9af1a..09806746b2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-5.3.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['536dbd82896d6facc16de8f961d17d65'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] dontcreateinstalldir = 'True' -- GitLab From e1d1dbbfa433cf1e5c52482d274fba80c8219468 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 09:22:01 +0200 Subject: [PATCH 677/722] {toolchain}[dummy] foss/2016.04 --- .../f/FFTW/FFTW-3.3.4-gompi-2016.04.eb | 34 +++++++++++++ easybuild/easyconfigs/f/foss/foss-2016.04.eb | 35 +++++++++++++ .../easyconfigs/g/gompi/gompi-2016.04.eb | 20 ++++++++ .../easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb | 18 +++++++ .../h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb | 23 +++++++++ .../numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb | 23 +++++++++ ...BLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 51 +++++++++++++++++++ .../OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb | 32 ++++++++++++ ...pi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb | 25 +++++++++ 9 files changed, 261 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2016.04.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2016.04.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb new file mode 100644 index 0000000000..aeee54992e --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2016.04'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.04.eb b/easybuild/easyconfigs/f/foss/foss-2016.04.eb new file mode 100644 index 0000000000..b70b879a23 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016.04.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016.04' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.3.0-2.26' + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('OpenMPI', '1.10.2', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb new file mode 100644 index 0000000000..b978fd902a --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.04' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.3.0-2.26' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC 5.3.0 and binutils 2.26 + ('OpenMPI', '1.10.2', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb new file mode 100644 index 0000000000..e65fa73eda --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2016.04'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..5a122dc923 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..d7d6d78efa --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..d8f2e33a19 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.18' + +lapackver = '3.6.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..4502f5c9f4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.11.3')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..326e2d8f43 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2016.04'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blassuff = '-LAPACK-3.6.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '5.3.0-2.26'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From d70cc438be3667d0aed78dc8ac353bbae6a3ad2d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 11:15:21 +0200 Subject: [PATCH 678/722] modify easyconfig Mathematica-10.4.1.eb --- .../m/Mathematica/Mathematica-10.4.1.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb new file mode 100644 index 0000000000..9d13deaf53 --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb @@ -0,0 +1,14 @@ +name = 'Mathematica' +version = '10.4.1' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%(version)s_LINUX.sh'] + +license_server = 'license.example.com' + +moduleclass = 'math' -- GitLab From 176ad0202e8ea0ec6bff115ce32aa1cbe5449d77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 12:59:05 +0200 Subject: [PATCH 679/722] add easyconfig FLANN-1.8.4-intel-2016a-Python-2.7.11.eb --- .../FLANN-1.8.4-intel-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..2072207364 --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.8.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cs.ubc.ca/research/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www.cs.ubc.ca/research/flann/uploads/FLANN/'] +sources = ['flann-%(version)s-src.zip'] + +builddependencies = [('CMake', '3.5.2')] +dependencies = [ + ('Python', '2.7.11'), +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/doc/flann', 'share/flann/python'], +} +sanity_check_commands = [('python', '-c "import pyflann"')] + +moduleclass = '' -- GitLab From a85f8ccc6a4f2eec679db0cbb58d270c32f0d0c0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 13:50:48 +0200 Subject: [PATCH 680/722] rm FIAT config --- .../FIAT-1.6.0-foss-2016a-Python-2.7.11.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index 649eb41225..0000000000 --- a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'FIAT' -version = '1.6.0' - -homepage = 'https://bitbucket.org/fenics-project/fiat' -description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order -instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating -arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] -sources = [SOURCELOWER_TAR_GZ] - -pyver = '2.7.11' -versionsuffix = '-Python-%s' % pyver - -dependencies = [ - ('Python', pyver), - ('sympy', '0.7.6.1', versionsuffix), -] - -options = {'modulename': name} - -pyshortver = '.'.join(pyver.split('.')[:2]) -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'math' -- GitLab From b34ef4de8733009684425ad8f39f0480f561a19e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:21:45 +0200 Subject: [PATCH 681/722] updated NASM and x264 --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb index b93565bb4f..0badebf4eb 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb @@ -12,9 +12,9 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ - ('NASM', '2.11.08'), + ('NASM', '2.12.01'), ('zlib', '1.2.8'), - ('x264', '20160114'), + ('x264', '20160430'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' -- GitLab From a88a6c7339fc37a4c19a29f58dc1ca32654d8383 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:24:38 +0200 Subject: [PATCH 682/722] NASM with foss 2016a --- .../n/NASM/NASM-2.12.01-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb new file mode 100644 index 0000000000..3097f4cb0e --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.01' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 0839e877fbd375b3c22f3901ed9e7870346343f4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:27:02 +0200 Subject: [PATCH 683/722] x264 with foss2016a --- .../x/x264/x264-20160430-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb new file mode 100644 index 0000000000..5f7b69a6bc --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160430' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 5fb8dea52cb48755a96ff45156087c5071e3fcf5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:28:15 +0200 Subject: [PATCH 684/722] for foss --- easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb index 5f7b69a6bc..7a55229c71 100644 --- a/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb +++ b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb @@ -7,7 +7,7 @@ homepage = 'http://www.videolan.org/developers/x264.html' description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.""" -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [ 'https://download.videolan.org/pub/videolan/x264/snapshots/', -- GitLab From 8caf1e4defeaff863d5b7205f6b1576e6837d914 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:31:35 +0200 Subject: [PATCH 685/722] FLASH with foss 2016a --- .../f/FLASH/FLASH-1.2.11-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb b/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb new file mode 100644 index 0000000000..5212c8b658 --- /dev/null +++ b/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'FLASH' +version = '1.2.11' + +homepage = 'https://ccb.jhu.edu/software/FLASH/' +description = """FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software + tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to + merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. + The resulting longer reads can significantly improve genome assemblies. They can also improve + transcriptome assembly when FLASH is used to merge RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://download.sourceforge.net/%(namelower)spage'] +sources = [SOURCE_TAR_GZ] + +files_to_copy = [(['flash'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/flash'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 486cc49fa3b8fda9c1a1d48d581e5decbe837fb8 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:50:56 +0200 Subject: [PATCH 686/722] Yasm with foss 2016a --- .../y/Yasm/Yasm-1.3.0-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb new file mode 100644 index 0000000000..fd9ab5e210 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From cc7240533ac882ca7bfc16fffa56d51c6fa4365d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 15:19:19 +0200 Subject: [PATCH 687/722] provided author and explaination for patch --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch index e0aa55dbeb..39bfb5c655 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch @@ -1,3 +1,6 @@ +# Remove use of -Werror because Werror is not used (discussed in http://seqanswers.com/forums/showthread.php?t=20113). +# Using -Werror gives warnings which result in a failure of the installation. +# Author: Fokke Dijkstra - Rijksuniversiteit Groningen (RUG) --- lastz-distrib-1.02.00/src/Makefile 2010-01-13 18:00:09.000000000 +0100 +++ lastz-distrib-1.02.00/src/Makefile 2015-02-09 17:22:41.030256461 +0100 @@ -28,7 +28,7 @@ -- GitLab From 2e74be2bf1817e6e33b78b68b394223cde42a32b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:07:40 +0200 Subject: [PATCH 688/722] add easyconfig PCL-1.7.2-intel-2016a-Python-2.7.11.eb, add easyconfig VTK-6.3.0-intel-2016a-Python-2.7.11.eb, add easyconfig Eigen-3.2.8-intel-2016a.eb --- .../e/Eigen/Eigen-3.2.8-intel-2016a.eb | 14 +++++ .../PCL-1.7.2-intel-2016a-Python-2.7.11.eb | 33 ++++++++++ .../VTK-6.3.0-intel-2016a-Python-2.7.11.eb | 60 +++++++++++++++++++ 3 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb new file mode 100644 index 0000000000..ec8373b9eb --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.8' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..6c685288a4 --- /dev/null +++ b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'PCL' +version = '1.7.2' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://pointclouds.org/' +description = """The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and + point cloud processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PointCloudLibrary/pcl/archive/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.5.2')] +dependencies = [ + ('Boost', '1.60.0', versionsuffix), + ('Eigen', '3.2.8'), + ('FLANN', '1.8.4', versionsuffix), + ('VTK', '6.3.0', versionsuffix), + ('Qhull', '2015.2'), +] + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include/pcl-%(version_major_minor)s/pcl', 'lib', 'share/pcl-%(version_major_minor)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1302e71e57 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,60 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '6.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.5.2')] + +mesaver = '11.0.8' +dependencies = [ + ('Python', '2.7.11'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', + 'mkg3states', 'ParseOGLExt']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' -- GitLab From da8956afd380f0e489f882180c6efea70d2d3955 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:23:20 +0200 Subject: [PATCH 689/722] drop toolchainopts from Eigen easyconfigs, since it is headers-only --- easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb | 1 - .../easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb | 1 - 22 files changed, 22 deletions(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb index a9cf345767..447fdcc2f1 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb index 57fad2e4e7..3cc61b8643 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb index 04a48d1f60..f64ca17dc1 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb index 34c32694d7..ad92c7352d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb index eda95916d0..c2159638f2 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb @@ -19,7 +19,6 @@ description = """Eigen is a C++ template library for linear algebra: toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb index ab4f378feb..0db2cb2232 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb index 92042e0a82..ad65bdfc92 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb index 5e8553cde7..8868b07c82 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb index bf81409418..0a2271f035 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb index 934d581d37..0dd48816d2 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb index 890a8a4839..9e7b9cf60d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb index 024205f8b6..7cbefdf8ab 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb index bca769f27d..81edc7d68b 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb index ab03a385a5..b3c186165b 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb index 9cca953ebc..d9a3a23dd0 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'foss', 'version': '2015a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb index d9ce74d1cf..fcb13a817f 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb index 5ec6f45b74..8648dbd440 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'dummy', 'version': ''} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb index ec09959b74..59832233f0 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb index 6d4de9bbd8..d79ef2b7af 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'dummy', 'version': ''} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb index a45d43c1fa..7d8ebf1a32 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb index 16eecd14b8..499d24c76f 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb index 5e2d4fc5a2..f02fff458c 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] -- GitLab From 01924fc6212f07e9a18cd600576f2a1672ee8442 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 16:46:57 +0200 Subject: [PATCH 690/722] quickfix --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb index 76b32edded..10dacf3472 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] -patches = ['LASTZ-1.02.00_Makefile.patch'] +patches = ['LASTZ-%(version)s_Makefile.patch'] skipsteps = ['configure'] -- GitLab From aacbf6070779e6cd532ce03bea9aee2da65ddc87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:47:51 +0200 Subject: [PATCH 691/722] modify easyconfig PCL-1.7.2-intel-2016a-Python-2.7.11.eb, modify easyconfig VTK-6.3.0-intel-2016a-Python-2.7.11.eb --- .../easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb | 2 +- .../easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb index 6c685288a4..2aa0797158 100644 --- a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ dependencies = [ ('Qhull', '2015.2'), ] -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts = '-DCMAKE_BUILD_TYPE=Release ' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb index 1302e71e57..55d38284a0 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb @@ -33,7 +33,6 @@ sources = [ builddependencies = [('CMake', '3.5.2')] -mesaver = '11.0.8' dependencies = [ ('Python', '2.7.11'), ('libGLU', '9.0.0', '-Mesa-11.2.1'), -- GitLab From b83826fbddbf3a82d2852de3a0ff3b372d7cafb2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:56:18 +0200 Subject: [PATCH 692/722] modify easyconfig Eigen-3.2.8-intel-2016a.eb --- easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb index ec8373b9eb..3ba31dc38d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] -- GitLab From 2cb4f18e397665dca42a2855989d8dc1c873f82d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:00:48 +0200 Subject: [PATCH 693/722] fix moduleclass in FLANN easyconfig --- .../f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb index 2072207364..82bf05536d 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb @@ -31,4 +31,4 @@ sanity_check_paths = { } sanity_check_commands = [('python', '-c "import pyflann"')] -moduleclass = '' +moduleclass = 'lib' -- GitLab From 85d18715306f40b7df042be06ace371577d0ddcc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:03:13 +0200 Subject: [PATCH 694/722] check moduleclass for all easyconfigs --- test/easyconfigs/easyconfigs.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index db5060f0b6..2d23e93e64 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -49,6 +49,7 @@ from easybuild.framework.easyconfig.easyconfig import get_easyblock_class from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, process_easyconfig from easybuild.tools import config +from easybuild.tools.config import build_option from easybuild.tools.filetools import write_file from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS @@ -263,8 +264,9 @@ def template_easyconfig_test(self, spec): fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) self.assertEqual(expected_subdir, subdir, fail_msg) - # sanity check for software name - self.assertTrue(ec['name'], name) + # sanity check for software name, moduleclass + self.assertEqual(ec['name'], name) + self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) -- GitLab From 8d70f76effbf87f18b59050f70ab2ac317a87e10 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 9 May 2016 17:05:41 +0200 Subject: [PATCH 695/722] Set additional environment variables needed by MDSplus --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 5 +++++ ...MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index b1dbee0965..111f00bfda 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -27,4 +27,9 @@ preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' parallel = 1 +modextravars = { + 'MDSPLUS_DIR': '%(installdir)s', + 'MDS_PATH': '%(installdir)s/tdi', +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb index a5aa488ebe..25d836f8e5 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -27,4 +27,9 @@ preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' parallel = 1 +modextravars = { + 'MDSPLUS_DIR': '%(installdir)s', + 'MDS_PATH': '%(installdir)s/tdi', +} + moduleclass = 'data' -- GitLab From c0da370258d724be5c96dbdebecaf64eee8d6359 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 17:33:50 +0200 Subject: [PATCH 696/722] drop double line --- .../b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index 2abd2af08c..a42f248efe 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -12,7 +12,6 @@ name = 'Biopython' version = '1.65' versionsuffix = "-Python-%(pyver)s" - homepage = 'http://www.biopython.org' description = """Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to @@ -35,4 +34,4 @@ sanity_check_paths = { options = {'modulename': 'Bio'} -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From 48e0528837d5a104c655550c908631e367632b41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:51:00 +0200 Subject: [PATCH 697/722] add easyconfig FFmpeg-3.0.2-intel-2016a.eb --- .../f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb new file mode 100644 index 0000000000..fb0c75a29b --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.0.2' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('x264', '20160430'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From 6a9be36285ea30558bf51ebf212608de44f13806 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:51:29 +0200 Subject: [PATCH 698/722] add easyconfig SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb --- ...iteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000..63fe3bdb3b --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb @@ -0,0 +1,24 @@ +name = 'SuiteSparse' +version = '4.5.2' + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' + +maxparallel = 1 + +moduleclass = 'numlib' -- GitLab From 013bc31badbb395d57449e5284215e61f826610d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 9 May 2016 19:10:28 +0100 Subject: [PATCH 699/722] add easyconfig FastQC-0.11.5-Java-1.7.0_80.eb, add easyconfig FastQC-0.11.5-Java-1.8.0_74.eb --- .../f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb | 32 +++++++++++++++++++ .../f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb create mode 100644 easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb new file mode 100644 index 0000000000..f6dbacc9e2 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] + +patches = ['FastQC_shebang.patch'] + +dependencies = [('Java', '1.7.0_80')] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] + +sanity_check_paths = { + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb new file mode 100644 index 0000000000..7b8be6500d --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] + +patches = ['FastQC_shebang.patch'] + +dependencies = [('Java', '1.8.0_74')] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] + +sanity_check_paths = { + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' -- GitLab From fa6d81bf60bb2cb4f1f582a8577b718d0e151665 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 12:53:28 +0200 Subject: [PATCH 700/722] Change to bundle, include CGI --- .../BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 29 ++++++++++++------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index fdb264f023..3e3a66a690 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -1,4 +1,4 @@ -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.6.924' @@ -10,21 +10,30 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] -sources = ['release-%s.tar.gz' % version.replace('.', '-')] +# this is a bundle of Perl modules packages +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") dependencies = [ ('Perl', '5.22.1'), ('DB_File', '1.835', versionsuffix), ] -#exts_list = [ -# ('CGI', '4.28', { -# 'source_tmpl': 'CGI-4.28.tar.gz', -# 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], -# }), -#] +exts_list = [ + ('CGI', '4.28', { + 'source_tmpl': 'CGI-4.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + }), + (name, version, { + 'modulename': 'Bio::Perl', + 'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'), + 'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'], + }), +] -options = {'modulename': 'Bio::Perl'} +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' +} moduleclass = 'bio' + -- GitLab From ea4d86d83894b1ec5cae01517b40c0a46df6f55d Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 12:56:36 +0200 Subject: [PATCH 701/722] Small change in comment --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 3e3a66a690..bd7bcac177 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -10,7 +10,7 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'foss', 'version': '2016a'} -# this is a bundle of Perl modules packages +# this is a bundle of Perl modules exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") -- GitLab From 5442266f3d9b5f6f62514c323f29b2dfd3724f96 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 13:02:34 +0200 Subject: [PATCH 702/722] Comment about CGI --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index bd7bcac177..796b828449 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -20,6 +20,7 @@ dependencies = [ ] exts_list = [ + # CGI has been removed from the Perl core since version 5.22. ('CGI', '4.28', { 'source_tmpl': 'CGI-4.28.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], -- GitLab From 6d2ee53436d7ffd21309097fd057bb8a99ddec77 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 13:04:17 +0200 Subject: [PATCH 703/722] Comment about CGI --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 796b828449..d62e2cbb88 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -20,7 +20,7 @@ dependencies = [ ] exts_list = [ - # CGI has been removed from the Perl core since version 5.22. + # CGI has been removed from the Perl core since version 5.22 ('CGI', '4.28', { 'source_tmpl': 'CGI-4.28.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], -- GitLab From 08cf383bee8935e7091cdec693c1fbba153ae5cd Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 10 May 2016 11:15:28 -0400 Subject: [PATCH 704/722] PGI: uncomment sanity checks; they now work with framework PR #1754 --- .../OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index be813ed50e..95cc4d76a5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -31,10 +31,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } -#sanity_check_commands = [ -# ('mpicc --version | grep pgcc', ''), -# ('mpicxx --version | grep pgc++', ''), -# ('mpifort --version | grep pgfortran', ''), -#] +sanity_check_commands = [ + ('mpicc --version | grep pgcc', ''), + ('mpicxx --version | grep pgc++', ''), + ('mpifort --version | grep pgfortran', ''), +] moduleclass = 'mpi' -- GitLab From a4703d9def18a0867167a45f1244c593099b1a79 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 10 May 2016 13:05:38 -0400 Subject: [PATCH 705/722] GraphicsMagick: add include/GraphicsMagick to CPATH as that is the include path. --- .../g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb | 2 ++ .../g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb | 2 ++ .../g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb index 513feabb7e..b7e2be06e2 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb @@ -14,4 +14,6 @@ source_urls = [ ] sources = [SOURCE_TAR_GZ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb index 6fa3747197..bd06dcc281 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb @@ -32,4 +32,6 @@ dependencies = [ ('zlib', '1.2.8'), ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb index ea37c3e81c..de4cfae31e 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb @@ -32,4 +32,6 @@ dependencies = [ ('zlib', '1.2.8'), ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' -- GitLab From 7184d0c0ddec1f80515700b43193c9721315b429 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Tue, 10 May 2016 15:33:50 -0400 Subject: [PATCH 706/722] add easyconfig CGAL 4.8 for foss 2016a and dependencies --- .../CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb | 33 ++++++++++++++++ .../e/expat/expat-2.1.1-foss-2016a.eb | 16 ++++++++ .../fontconfig-2.11.95-foss-2016a.eb | 22 +++++++++++ .../intltool-0.51.0-foss-2016a-Perl-5.22.1.eb | 25 ++++++++++++ .../libxkbcommon-0.6.1-foss-2016a.eb | 32 +++++++++++++++ .../m/MPFR/MPFR-3.1.4-foss-2016a.eb | 26 +++++++++++++ .../easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb | 39 +++++++++++++++++++ .../XKeyboardConfig-2.17-foss-2016a.eb | 36 +++++++++++++++++ .../XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb | 27 +++++++++++++ .../xcb-util-image-0.4.0-foss-2016a.eb | 23 +++++++++++ .../xcb-util-keysyms-0.4.0-foss-2016a.eb | 24 ++++++++++++ .../xcb-util-renderutil-0.3.9-foss-2016a.eb | 23 +++++++++++ .../xcb-util-wm-0.4.1-foss-2016a.eb | 23 +++++++++++ .../x/xcb-util/xcb-util-0.4.0-foss-2016a.eb | 24 ++++++++++++ 14 files changed, 373 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f4633df398 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +name = 'CGAL' +version = '4.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['e31e7039b5cdc74ac7b106db8ba644f3'] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('MPFR', '3.1.4'), + ('Qt5', '5.6.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.5.2'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000..1a58effe3d --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.1' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb new file mode 100644 index 0000000000..93a5699fb5 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.95' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.1'), + ('freetype', '2.6.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..e0b8aa4117 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.22.1' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.44', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb new file mode 100644 index 0000000000..5f450a0988 --- /dev/null +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxkbcommon' +version = '0.6.1' + +homepage = 'http://xkbcommon.org/' +description = """xkbcommon is a library to handle keyboard descriptions, + including loading them from disk, parsing them and handling their state. + It's mainly meant for client toolkits, window systems, + and other system applications.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xkbcommon.org/download/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libxcb', '1.11.1'), + ('XKeyboardConfig', '2.17'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': ['lib/libxkbcommon%s.so' % x for x in ['', '-x11']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb new file mode 100644 index 0000000000..fe347368b1 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.0')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb new file mode 100644 index 0000000000..27b1514a37 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.6.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +dependencies = [ + ('GLib', '2.48.0'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXi', '1.7.6'), + ('xcb-util', '0.4.0'), + ('xcb-util-image', '0.4.0'), + ('xcb-util-keysyms', '0.4.0'), + ('xcb-util-renderutil', '0.3.9'), + ('xcb-util-wm', '0.4.1'), + ('libxkbcommon', '0.6.1'), + ('libXrender', '0.9.9'), + ('fontconfig', '2.11.95'), + ('freetype', '2.6.3'), + ('libXfixes', '5.0.1'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('libXrandr', '1.5.0'), + ('libpng', '1.6.21'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb new file mode 100644 index 0000000000..10d7fbd3ea --- /dev/null +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'XKeyboardConfig' +version = '2.17' + +homepage = 'http://www.freedesktop.org/wiki/Software/XKeyboardConfig/' +description = """The non-arch keyboard configuration database for X Window. + The goal is to provide the consistent, well-structured, + frequently released open source of X keyboard configuration data + for X Window System implementations (free, open source and commercial). + The project is targeted to XKB-based systems.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://ftp.x.org/pub/individual/data/xkeyboard-config/'] +sources = ['xkeyboard-config-%(version)s.tar.bz2'] + +builddependencies = [ + ('libxslt', '1.1.28'), + ('gettext', '0.19.7'), + ('intltool', '0.51.0', '-Perl-5.22.1'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +# see http://www.linuxfromscratch.org/blfs/view/svn/x/xkeyboard-config.html +configopts = '--with-xkb-rules-symlink=xorg ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/X11/xkb'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..71416dbf17 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.44' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1'), + ('expat', '2.1.1') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb new file mode 100644 index 0000000000..bb023fe417 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-image' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-image package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('xcb-util', '0.4.0'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-image.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb new file mode 100644 index 0000000000..000b28f309 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-keysyms' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-keysyms package contains a library for + handling standard X key constants and conversion to/from keycodes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-keysyms.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb new file mode 100644 index 0000000000..fd3484fb38 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-renderutil' +version = '0.3.9' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-renderutil package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-render-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb new file mode 100644 index 0000000000..d412a4babf --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-wm' +version = '0.4.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-%s.so' % x for x in ['ewmh', 'icccm']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb new file mode 100644 index 0000000000..78a0c3a9b7 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util package provides additional extensions to the XCB library, + many that were previously found in Xlib, but are not part of core X protocol""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From dfabd2e04531e4f26aa54f3d487e36da8774b93c Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Tue, 10 May 2016 15:40:40 -0400 Subject: [PATCH 707/722] add easyconfig boost_versionsuffix --- .../Boost-1.60.0-foss-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a913c20849 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.60.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 6569ffa0d96ffcf7dfe5545df6567d0eb19d2b51 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 May 2016 14:00:02 +0200 Subject: [PATCH 708/722] {bio}[foss-2016a] Kraken 0.10.5-beta (REVIEW) --- .../Jellyfish/Jellyfish-1.1.11-foss-2016a.eb | 25 +++++++++++ ...aken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 43 +++++++++++++++++++ .../Kraken/Kraken_0.10.5-beta_makefile.patch | 12 ++++++ 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb new file mode 100644 index 0000000000..8e2a518511 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '1.1.11' + +homepage = 'http://www.cbcb.umd.edu/software/jellyfish/' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cbcb.umd.edu/software/jellyfish/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..ad490e94ef --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PackedBinary' + +name = 'Kraken' +version = '0.10.5-beta' +versionsuffix='-Perl-%(perlver)s' + +homepage = 'http://ccb.jhu.edu/software/kraken/' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +#Part is compiled with CXX, the rest is in Perl +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://ccb.jhu.edu/software/kraken/dl/'] +sources = [SOURCELOWER_TGZ] + +patches = ['Kraken_%(version)s_makefile.patch'] + +dependencies = [ + ('Perl', '5.22.1'), + ('Jellyfish', '1.1.11'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken.sh %(installdir)s' + +sanity_check_paths = { + 'files': ['add_to_library.sh', 'build_kraken_db.sh', 'check_for_jellyfish.sh', 'classify', 'clean_db.sh', + 'cp_into_tempfile.pl', 'db_shrink', 'db_sort', 'download_genomic_library.sh', + 'download_taxonomy.sh', 'kraken', 'kraken-build', 'kraken-filter', 'krakenlib.pm', + 'kraken-mpa-report', 'kraken-report', 'kraken-translate', 'make_seqid_to_taxid_map', + 'read_merger.pl', 'report_gi_numbers.pl', 'set_lcas', 'shrink_db.sh', + 'standard_installation.sh', 'upgrade_db.sh', 'verify_gi_numbers.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch b/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch new file mode 100644 index 0000000000..4a0bc26aa6 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch @@ -0,0 +1,12 @@ +#Pick CXX and CXXFLAGS from EasyBuild via pre-defined variables +#May 11th 2016 by B. Hajgato (Free Uninrrsity Brussels, VUB) +--- kraken-0.10.5-beta/src/Makefile.orig 2015-02-18 12:38:00.000000000 +0100 ++++ kraken-0.10.5-beta/src/Makefile 2016-05-11 13:33:39.370016057 +0200 +@@ -1,5 +1,5 @@ +-CXX = g++ +-CXXFLAGS = -Wall -fopenmp -O3 ++CXX ?= g++ ++CXXFLAGS ?= -Wall -fopenmp -O3 + PROGS = db_sort set_lcas classify make_seqid_to_taxid_map db_shrink + + .PHONY: all install clean -- GitLab From e6a548baeec911151b309f32cc10404060136fb6 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 11 May 2016 15:04:52 +0200 Subject: [PATCH 709/722] Add OpenSSL-1.0.2g-GCCcore-4.9.3.eb to work with minimal toolchains --- .../o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..29256de39d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.2g' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From ee694e1b8f698196b590aaee777130a1feb3de1f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 11 May 2016 16:09:49 +0200 Subject: [PATCH 710/722] Add tmux-2.2-GCCcore-4.9.3.eb --- .../t/tmux/tmux-2.2-GCCcore-4.9.3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..a8b6500ba3 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '2.2' + +homepage = 'http://tmux.sourceforge.net/' +description = """tmux is a terminal multiplexer. It lets you switch easily +between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + +dependencies = [ + ('ncurses', '6.0'), + ('libevent', '2.0.22'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 8a22b902332cf5110c9055b9df18c2d720522d93 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 11 May 2016 16:10:06 +0200 Subject: [PATCH 711/722] Add libevent-2.0.22-GCCcore-4.9.3.eb --- .../libevent/libevent-2.0.22-GCCcore-4.9.3.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..2de9d3663c --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.0.22' + +homepage = 'http://libevent.org/' +description = """The libevent API provides a mechanism to execute a callback function when a specific + event occurs on a file descriptor or after a timeout has been reached. + Furthermore, libevent also support callbacks due to signals or regular timeouts.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = [ + 'https://github.com/downloads/%(name)s/%(name)s/', + 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', +] +sources = ['%(name)s-%(version)s-stable.tar.gz'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + +moduleclass = 'lib' -- GitLab From f280305bef61512ee04bf405afee98cb1d9e2802 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 May 2016 16:20:40 +0200 Subject: [PATCH 712/722] add wget dependency to Kraken --- .../g/gnutls/gnutls-3.4.11-foss-2016a.eb | 40 +++++++++++++++++++ .../g/guile/guile-1.8.8-foss-2016a.eb | 32 +++++++++++++++ ...aken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 1 + .../l/libidn/libidn-1.32-foss-2016a.eb | 19 +++++++++ .../l/libtasn1/libtasn1-4.7-foss-2016a.eb | 22 ++++++++++ .../libunistring-0.9.3-foss-2016a.eb | 24 +++++++++++ .../n/nettle/nettle-3.1.1-foss-2016a.eb | 28 +++++++++++++ .../p/p11-kit/p11-kit-0.23.2-foss-2016a.eb | 29 ++++++++++++++ .../w/wget/wget-1.17.1-foss-2016a.eb | 35 ++++++++++++++++ 9 files changed, 230 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb new file mode 100644 index 0000000000..fbf5215dd8 --- /dev/null +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'gnutls' +version = '3.4.11' + +homepage = 'http://www.gnutls.org/' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCE_TAR_XZ] + +guilever = '1.8.8' +guileshortver = '.'.join(guilever.split('.')[:2]) +dependencies = [ + ('GMP', '6.1.0'), + ('nettle', '3.1.1'), + ('guile', guilever), + ('libtasn1', '4.7'), + ('libidn', '1.32'), + ('p11-kit', '0.23.2'), +] + +configopts = "--with-guile-site-dir=$EBROOTGUILE --enable-openssl-compatibility " + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['certtool', 'crywrap', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]] + + ['lib/guile/%s/guile-gnutls-v-2.so' % guileshortver], + 'dirs': ['include/gnutls'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb new file mode 100644 index 0000000000..132fe56abf --- /dev/null +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.0'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.29'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb index ad490e94ef..4bb09cbfe2 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -25,6 +25,7 @@ patches = ['Kraken_%(version)s_makefile.patch'] dependencies = [ ('Perl', '5.22.1'), ('Jellyfish', '1.1.11'), + ('wget', '1.17.1'), ] install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb new file mode 100644 index 0000000000..be095e8cc2 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.32' + +homepage = 'http://www.gnu.org/software/libidn' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb new file mode 100644 index 0000000000..0a37b2e392 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.7' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. + It was written by Fabio Fiorina, and has been shipped as part of GnuTLS + for some time but is now a proper GNU package.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb new file mode 100644 index 0000000000..052063704a --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb new file mode 100644 index 0000000000..fc3be53324 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.1.1' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb new file mode 100644 index 0000000000..75ecf0ad6a --- /dev/null +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'p11-kit' +version = '0.23.2' + +homepage = 'http://p11-glue.freedesktop.org/p11-kit.html' +description = """Provides a way to load and enumerate PKCS#11 modules. + Provides a standard configuration setup for installing + PKCS#11 modules in such a way that they're discoverable. + Also solves problems with coordinating the use of PKCS#11 + by different components or libraries living in the same process.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://p11-glue.freedesktop.org/releases/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libtasn1', '4.7'), + ('libffi', '3.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/p11-kit', 'bin/trust'] + + ['lib/libp11-kit.%s' % SHLIB_EXT], + 'dirs': ['include/p11-kit-1/p11-kit'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb new file mode 100644 index 0000000000..855ecb2068 --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.17.1' + +homepage = 'https://www.gnu.org/software/wget/' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('gnutls', '3.4.11'), + ('PCRE', '8.38'), + ('libidn', '1.32'), + ('zlib', '1.2.8'), + #('OpenSSL', '1.0.1s'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +#Optionally, you can use OpenSSL insted of gnutls +#configopts = '--with-ssl=openssl ' +# +#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/wget'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 7a5bbbf4be73ddcce4a1e18aa9dd2363fb5ce7f7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 May 2016 16:32:43 +0200 Subject: [PATCH 713/722] use os dep gnutls --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 855ecb2068..6ca8a613aa 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -14,7 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] dependencies = [ - ('gnutls', '3.4.11'), + #('gnutls', '3.4.11'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date gnutls for security reasons ('PCRE', '8.38'), ('libidn', '1.32'), ('zlib', '1.2.8'), @@ -26,6 +27,7 @@ dependencies = [ #configopts = '--with-ssl=openssl ' # #osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('gnutls')] sanity_check_paths = { 'files': ['bin/wget'], -- GitLab From 38cacab3b3d32d4b13267a167a6681e01a122d8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 16:53:18 +0200 Subject: [PATCH 714/722] add easyconfig Wannier90-2.0.1-intel-2016a.eb --- .../Wannier90/Wannier90-2.0.1-intel-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb new file mode 100644 index 0000000000..5f4964f921 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '2.0.1' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] + +patches = ['Wannier90_2x_ignore_makesys.patch'] + +prebuildopts = 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' + +# build program and library +buildopts = "all" + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' -- GitLab From 47ee49d3fe6431cb7a0f1b20a8778569f9c5db65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 16:53:43 +0200 Subject: [PATCH 715/722] add easyconfig FLEUR-0.26e-intel-2016a.eb --- .../f/FLEUR/FLEUR-0.26e-intel-2016a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb new file mode 100644 index 0000000000..39ac2cdb63 --- /dev/null +++ b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'FLEUR' +version = '0.26e' + +homepage = 'http://www.flapw.de/' +description = """FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, + based on density-functional theory.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +# dowload requires registration, see http://www.flapw.de/pm/index.php?n=FLEUR.Downloads +sources = ['v%s.tgz' % version.split('.')[1]] + +builddependencies = [('imake', '1.0.7')] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), + ('HDF5', '1.8.16'), +# ('Wannier90', '2.0.1'), # only needed if '#define wann' is added to Imakefile +] + +# define hardware platform to be 'parallel intel compiler, 64 bit, use scalapack') +prebuildopts = "sed -i 's/^#define jureca/#define linux_evp_64/g' Imakefile && " +# don't specialize for systems with structural symmetry +prebuildopts += "sed -i 's/^#define inversion//g' Imakefile && " +# no need to jump through hoops to make compilation work with older Fortran compilers +prebuildopts += "sed -i 's/^#define f_90//g' Imakefile && " + +prebuildopts += "imake && " +buildopts = 'FC="$FC" FFLAGS="$FFLAGS -r8 -assume byterecl" HDFROOT=$EBROOTHDF5 fleur.x inpgen.x' + +# parallel build tends to fail +parallel = 1 + +files_to_copy = [(['fleur.x', 'inpgen.x'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fleur.x', 'bin/inpgen.x'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From b34283cba9fb1d3ccea409d2e7fc8a885fe13d30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 20:30:33 +0200 Subject: [PATCH 716/722] fix remark, enable r8 toolchain option, add imake easyconfig to resolve dep --- .../f/FLEUR/FLEUR-0.26e-intel-2016a.eb | 4 ++-- .../i/imake/imake-1.0.7-intel-2016a.eb | 21 +++++++++++++++++++ 2 files changed, 23 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb index 39ac2cdb63..d7d711211d 100644 --- a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb @@ -8,7 +8,7 @@ description = """FLEUR is a feature-full, freely available FLAPW (full potential based on density-functional theory.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'r8': True} # dowload requires registration, see http://www.flapw.de/pm/index.php?n=FLEUR.Downloads sources = ['v%s.tgz' % version.split('.')[1]] @@ -30,7 +30,7 @@ prebuildopts += "sed -i 's/^#define inversion//g' Imakefile && " prebuildopts += "sed -i 's/^#define f_90//g' Imakefile && " prebuildopts += "imake && " -buildopts = 'FC="$FC" FFLAGS="$FFLAGS -r8 -assume byterecl" HDFROOT=$EBROOTHDF5 fleur.x inpgen.x' +buildopts = 'FC="$FC" FFLAGS="$FFLAGS" HDFROOT=$EBROOTHDF5 fleur.x inpgen.x' # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb new file mode 100644 index 0000000000..dd473f56b9 --- /dev/null +++ b/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'imake' +version = '1.0.7' + +homepage = 'http://www.x.org/' +description = """imake is a Makefile-generator that is intended to make it easier to develop software + portably for multiple systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['ftp://artfiles.org/x.org/pub/individual/util/'] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['ccmakedep', 'cleanlinks', 'imake', 'makeg', 'mergelib', + 'mkdirhier', 'mkhtmlindex', 'revpath', 'xmkmf']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ffd9ea76ab826db4b79c77d1901733df17239d59 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 May 2016 07:38:23 +0200 Subject: [PATCH 717/722] Use OpenSSL --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 6ca8a613aa..969681ed3b 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -23,11 +23,11 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -#Optionally, you can use OpenSSL insted of gnutls -#configopts = '--with-ssl=openssl ' -# -#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -osdependencies = [('gnutls')] +configopts = '--with-ssl=openssl ' + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +#Optionally, you can use gnutls (default) instead of OpenSSL +#osdependencies = [('gnutls-devel', 'gnutls-dev), 'libgnutls-devel')] sanity_check_paths = { 'files': ['bin/wget'], -- GitLab From f4491d2ac003c2e3b16e422b837043762403c720 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 May 2016 09:29:40 +0200 Subject: [PATCH 718/722] Type corrected in the comment --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 969681ed3b..462167df50 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -26,8 +26,8 @@ dependencies = [ configopts = '--with-ssl=openssl ' osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -#Optionally, you can use gnutls (default) instead of OpenSSL -#osdependencies = [('gnutls-devel', 'gnutls-dev), 'libgnutls-devel')] +#Optionally, you can use gnutls (default) instead of OpenSSL +#osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] sanity_check_paths = { 'files': ['bin/wget'], -- GitLab From b4850c38476a83f68723becde0c0d16646849551 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 May 2016 09:32:05 +0200 Subject: [PATCH 719/722] extra comment --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 462167df50..bbebd9aa83 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -26,7 +26,8 @@ dependencies = [ configopts = '--with-ssl=openssl ' osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -#Optionally, you can use gnutls (default) instead of OpenSSL +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. #osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] sanity_check_paths = { -- GitLab From 3fbfc03ba64a14c5c803d6761009142a490e5015 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 10:57:41 +0200 Subject: [PATCH 720/722] {chem}[intel/2016a] NBO 1.1 --- .../easyconfigs/n/NBO/NBO-1.1_MKL95.patch | 505 ++++++++++++++++++ easybuild/easyconfigs/n/NBO/NBO.eb | 27 + 2 files changed, 532 insertions(+) create mode 100644 easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch create mode 100644 easybuild/easyconfigs/n/NBO/NBO.eb diff --git a/easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch b/easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch new file mode 100644 index 0000000000..1bde9b006b --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch @@ -0,0 +1,505 @@ +fix using BLAS95/LAPACK95 interface for recent Intel MKL versions +author: Kenneth Hoste (HPC-UGent) +diff -ru periodic_nbo.orig/matutil.f90 periodic_nbo/matutil.f90 +--- periodic_nbo.orig/matutil.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/matutil.f90 2016-05-12 10:17:54.673546000 +0200 +@@ -93,7 +93,7 @@ + END FUNCTION matdet + + FUNCTION matsqrt_real(dmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matsqrt_real, vecs +@@ -115,14 +115,14 @@ + FORALL (i=1:n1) matsqrt_real(i,i) = SQRT(abs(vals(i))) + !matsqrt_real = MATMUL(vecs, MATMUL(matsqrt_real, TRANSPOSE(vecs))) + +- CALL DGEMM_MKL95(vecs,matsqrt_real,dummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,vecs,matsqrt_real,'N','T',1.d0,0.d0) ++ CALL DGEMM(vecs,matsqrt_real,dummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(dummy,vecs,matsqrt_real,'N','T',1.d0,0.d0) + + + END FUNCTION matsqrt_real + + FUNCTION matsqrt_complex(cmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + COMPLEX*16 , DIMENSION(SIZE(cmat,1),SIZE(cmat,2)) :: matsqrt_complex, vecs +@@ -140,13 +140,13 @@ + FORALL (i=1:n1) matsqrt_complex(i,i) = SQRT(abs(vals(i))) + !matsqrt_complex = MATMUL(vecs, MATMUL(matsqrt_complex, TRANSPOSE(CONJG(vecs)))) + +- CALL ZGEMM_MKL95(vecs,matsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(dummy,vecs,matsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(vecs,matsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(dummy,vecs,matsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + + END FUNCTION matsqrt_complex + + FUNCTION matinvsqrt_real(dmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matinvsqrt_real, vecs +@@ -164,13 +164,13 @@ + FORALL (i=1:n1) matinvsqrt_real(i,i) = 1.d0/SQRT(abs(vals(i))) + !matinvsqrt_real = MATMUL(vecs, MATMUL(matinvsqrt_real, TRANSPOSE(vecs))) + +- CALL DGEMM_MKL95(vecs,matinvsqrt_real,dummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,vecs,matinvsqrt_real,'N','T',1.d0,0.d0) ++ CALL DGEMM(vecs,matinvsqrt_real,dummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(dummy,vecs,matinvsqrt_real,'N','T',1.d0,0.d0) + + END FUNCTION matinvsqrt_real + + FUNCTION matinvsqrt_complex(cmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + COMPLEX*16 , DIMENSION(SIZE(cmat,1),SIZE(cmat,2)) :: matinvsqrt_complex, vecs +@@ -199,13 +199,13 @@ + + !matinvsqrt_complex = MATMUL(vecs, MATMUL(matinvsqrt_complex, TRANSPOSE(CONJG(vecs)))) + +- CALL ZGEMM_MKL95(vecs,matinvsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(dummy,vecs,matinvsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(vecs,matinvsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(dummy,vecs,matinvsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + + END FUNCTION matinvsqrt_complex + + FUNCTION matexp(dmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matexp, vecs +@@ -222,8 +222,8 @@ + matexp = 0.d0 + FORALL (i=1:n1) matexp(i,i) = EXP(vals(i)) + !matexp = MATMUL(vecs, MATMUL(matexp, TRANSPOSE(vecs))) +- CALL DGEMM_MKL95(vecs,matexp,dummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,vecs,matexp,'N','T',1.d0,0.d0) ++ CALL DGEMM(vecs,matexp,dummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(dummy,vecs,matexp,'N','T',1.d0,0.d0) + + END FUNCTION matexp + +@@ -246,8 +246,8 @@ + + ! solves the generalized eigenvalue equations D c=S c*lambda + SUBROUTINE diag_general(dmat,smat,dvals,dvecs) +- USE MKL95_BLAS +- USE MKL95_LAPACK ++ USE BLAS95 ++ USE LAPACK95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat, smat, dvecs + REAL*8 , DIMENSION(:) :: dvals +@@ -277,14 +277,14 @@ + + ! transform to the coordinates of the normal eigensystem + !dmat = MATMUL(TRANSPOSE(shalfi),MATMUL(dmat,shalfi)) +- CALL DGEMM_MKL95(shalfi,dmat,dummy,'T','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,shalfi,dmat,'N','N',1.d0,0.d0) ++ CALL DGEMM(shalfi,dmat,dummy,'T','N',1.d0,0.d0) ++ CALL DGEMM(dummy,shalfi,dmat,'N','N',1.d0,0.d0) + ! get the normal eigenvalues and vectors + call jacobi(dmat,n1,n1,dvals,dvecs,nrot) + ! transform the eigenvectors BACK to the original coordinate system + !dvecs = MATMUL(shalfi, dvecs) + dummy = dvecs +- CALL DGEMM_MKL95(shalfi,dummy,dvecs,'N','N',1.d0,0.d0) ++ CALL DGEMM(shalfi,dummy,dvecs,'N','N',1.d0,0.d0) + CALL eigsrt(dvals,dvecs,n1,n1) + + !WRITE(6,*)'Eigenvalues' +@@ -294,7 +294,7 @@ + END SUBROUTINE diag_general + + FUNCTION matinv_real(dmat) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matinv_real +@@ -306,12 +306,12 @@ + IF (n1.NE.n2) STOP 'Attempting to invert a non-square matrix' + + matinv_real=dmat +- CALL DGETRF_MKL95(matinv_real,ipiv,info) +- CALL DGETRI_MKL95(matinv_real,ipiv,info) ++ CALL DGETRF(matinv_real,ipiv,info) ++ CALL DGETRI(matinv_real,ipiv,info) + END FUNCTION matinv_real + + FUNCTION matinv_complex(cmat) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + COMPLEX*16 , DIMENSION(SIZE(cmat,1),SIZE(cmat,2)) :: matinv_complex +@@ -328,7 +328,7 @@ + + + !evecs = cmat +- !CALL ZHEEV_MKL95(evecs,evals,'V','U',INFO) ++ !CALL ZHEEV(evecs,evals,'V','U',INFO) + !DO info=1,SIZE(evals,1) + ! WRITE(6,'(F10.5)')evals(info) + !ENDDO +@@ -337,8 +337,8 @@ + + + matinv_complex=cmat +- CALL ZGETRF_MKL95(matinv_complex,ipiv,info) +- CALL ZGETRI_MKL95(matinv_complex,ipiv,info) ++ CALL ZGETRF(matinv_complex,ipiv,info) ++ CALL ZGETRI(matinv_complex,ipiv,info) + END FUNCTION matinv_complex + + FUNCTION outer_product(x,y) +@@ -351,7 +351,7 @@ + + !Fortran 90 wrappers for diag routines + SUBROUTINE matdiag_real(dmat,evals,evecs) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1)) :: evals +@@ -363,7 +363,7 @@ + IF (n1.NE.n2) STOP 'Attempting to diagonalize a non-square matrix' + + evecs=dmat +- !CALL dsyev_mkl95(evecs,evals,'V','U',info) ++ !CALL dsyev(evecs,evals,'V','U',info) + CALL diag(dmat,n1,n1,evals,evecs) + + !WRITE(6,*)'using real symmetrizing routine' +@@ -373,7 +373,7 @@ + END SUBROUTINE matdiag_real + + SUBROUTINE matdiag_complex(cmat,evals,evecs) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + REAL*8 , DIMENSION(SIZE(cmat,1)) :: evals +@@ -389,11 +389,11 @@ + + evecs=cmat + +- CALL zheev_mkl95(evecs,evals,'V','U',info) ++ CALL zheev(evecs,evals,'V','U',info) + IF (info.NE.0) STOP 'Error in matdiag_complex' + + !dummy=cmat +- !CALL ZGESVD_MKL95(dummy,sing_value,u_matrix,v_matrix) ++ !CALL ZGESVD(dummy,sing_value,u_matrix,v_matrix) + + + !IF( evals(1) .LE. -1.d-13 )WRITE(6,*)'WHOOOOOOOOOAAAAAAAAAAAAAAA!!! Negative eigenvalues' +@@ -436,31 +436,31 @@ + END FUNCTION matiden + + FUNCTION matunitary_trans_real(A,U) RESULT(Ap) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:) :: A,U + REAL*8,DIMENSION(SIZE(U,1),SIZE(U,1)) :: Ap + REAL*8,DIMENSION(SIZE(A,1),SIZE(U,1)) :: dummy + + !Ap=MATMUL(U,MATMUL(A,TRANSPOSE(U))) +- CALL DGEMM_MKL95(A,U,dummy,'N','T',1.d0,0.d0) +- CALL DGEMM_MKL95(U,dummy,Ap,'N','N',1.d0,0.d0) ++ CALL DGEMM(A,U,dummy,'N','T',1.d0,0.d0) ++ CALL DGEMM(U,dummy,Ap,'N','N',1.d0,0.d0) + END FUNCTION matunitary_trans_real + + FUNCTION matunitary_trans_complex(A,U) RESULT(Ap) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16,DIMENSION(:,:) :: A,U + COMPLEX*16,DIMENSION(SIZE(U,1),SIZE(U,1)) :: Ap + COMPLEX*16,DIMENSION(SIZE(A,1),SIZE(U,1)) :: dummy + + !Ap=MATMUL(U,MATMUL(A,CONJG(TRANSPOSE(U)))) +- CALL ZGEMM_MKL95(A,U,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(U,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(A,U,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(U,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + END FUNCTION matunitary_trans_complex + + FUNCTION matunitary_trans_complex2(A,U) RESULT(Ap) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16,DIMENSION(:,:) :: A + REAL*8,DIMENSION(:,:) :: U +@@ -470,8 +470,8 @@ + + U_comp = U + !Ap=MATMUL(U,MATMUL(A,TRANSPOSE(U))) +- CALL ZGEMM_MKL95(A,U_comp,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(U_comp,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(A,U_comp,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(U_comp,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + END FUNCTION matunitary_trans_complex2 + + +diff -ru periodic_nbo.orig/nbo.f90 periodic_nbo/nbo.f90 +--- periodic_nbo.orig/nbo.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/nbo.f90 2016-05-12 09:55:32.463039731 +0200 +@@ -1,6 +1,6 @@ + MODULE nbo + USE nbo_shared +- USE MKL95_BLAS ++ USE BLAS95 + PRIVATE + PUBLIC :: do_nbo, output + +@@ -336,7 +336,7 @@ + !IF( jg /= ig )Pi = Pi - outer_product(bond_coeff(:,2*ibondorlp+1-inbo,jg),bond_coeff(:,2*ibondorlp+1-inbo,jg)) + !proj_dummy = P + !P = MATMUL(Pi,P) +- !CALL DGEMM_MKL95(Pi,proj_dummy,P,'N','N',1.d0,0.d0) ++ !CALL DGEMM(Pi,proj_dummy,P,'N','N',1.d0,0.d0) + + rhoat=0.d0 + rhoat(iifirst:iilast,iifirst:iilast)=inp%rho0(ifirst:ilast,ifirst:ilast,ig,ispin) +@@ -379,8 +379,8 @@ + + !Now project out all of the bonding and antibonding density, to leave solely the dentisy associated with Rydberg states + !inp%rho0(:,:,1) = MATMUL(P,(MATMUL(inp%rho0(:,:,1),P))) +- !CALL DGEMM_MKL95(inp%rho0(:,:,1),P,proj_dummy,'N','N',1.d0,0.d0) +- !CALL DGEMM_MKL95(P,proj_dummy,inp%rho0(:,:,1),'N','N',1.d0,0.d0) ++ !CALL DGEMM(inp%rho0(:,:,1),P,proj_dummy,'N','N',1.d0,0.d0) ++ !CALL DGEMM(P,proj_dummy,inp%rho0(:,:,1),'N','N',1.d0,0.d0) + + + !PRINT *, 'made it to doing rydberg search' +@@ -552,7 +552,7 @@ + Pi=Pi-outer_product(lpcontrib,lpcontrib) + Pdummy=P + !P=MATMUL(Pi,P) +- CALL DGEMM_MKL95(Pi,Pdummy,P,'N','N',1.d0,0.d0) ++ CALL DGEMM(Pi,Pdummy,P,'N','N',1.d0,0.d0) + + !IF( occ > core_thresh*DBLE(3-inp%nspins) )THEN + ! PRINT *, 'Removing CR from atom',iatom +@@ -563,8 +563,8 @@ + !PRINT * + + !inp%rho0(:,:,1) = MATMUL(P,(MATMUL(inp%rho0(:,:,1),P))) +- CALL DGEMM_MKL95(inp%rho0(:,:,1,ispin),P,Pdummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(P,Pdummy,inp%rho0(:,:,1,ispin),'N','N',1.d0,0.d0) ++ CALL DGEMM(inp%rho0(:,:,1,ispin),P,Pdummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(P,Pdummy,inp%rho0(:,:,1,ispin),'N','N',1.d0,0.d0) + + + END SUBROUTINE do_1c_search +@@ -966,7 +966,7 @@ + + FUNCTION schmidt_orthog_matrix(S,n) RESULT(Os) + USE matutil +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:) :: S + REAL*8,DIMENSION(n,n) :: Sinv +@@ -981,7 +981,7 @@ + !onto the remaining basis function n+1:nbasis + Sinv=matinv(S(1:n,1:n)) + !proj=MATMUL(Sinv,S(1:n,n+1:nbasis)) +- CALL DGEMM_MKL95(Sinv,S(1:n,n+1:nbasis),proj,'N','N',1.d0,0.d0) ++ CALL DGEMM(Sinv,S(1:n,n+1:nbasis),proj,'N','N',1.d0,0.d0) + + !Now do gs orthogonalization using those projections + Os=0.d0 +diff -ru periodic_nbo.orig/nbo_shared.f90 periodic_nbo/nbo_shared.f90 +--- periodic_nbo.orig/nbo_shared.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/nbo_shared.f90 2016-05-12 09:55:32.463039731 +0200 +@@ -151,7 +151,7 @@ + !Calculates the number of electrons in the unit cell + ! + SUBROUTINE calc_nelec(inp,is_orthog) +- USE MKL95_BLAS ++ USE BLAS95 + USE matutil + IMPLICIT NONE + TYPE(nbo_input) :: inp +@@ -167,9 +167,9 @@ + + DO ispin=1,inp%nspins + DO ik=1,nk +- CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),inp%sk(:,:,ik),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(inp%rhok(:,:,ik,ispin),inp%sk(:,:,ik),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + nelec=nelec+inp%kpt_wt(ik)*mattrace(nelec_dummy) +- CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + nenergy=nenergy+inp%kpt_wt(ik)*mattrace(nelec_dummy) + ENDDO + ENDDO +diff -ru periodic_nbo.orig/periodic_matutil.f90 periodic_nbo/periodic_matutil.f90 +--- periodic_nbo.orig/periodic_matutil.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/periodic_matutil.f90 2016-05-12 09:55:32.463039731 +0200 +@@ -41,7 +41,7 @@ + !Multiples two periodic matrices. + ! + FUNCTION periodic_matmul(a,b) RESULT(c) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:,:), INTENT(in) :: a,b + REAL*8,DIMENSION(SIZE(a,1),SIZE(a,2),SIZE(a,3)) :: c +@@ -101,7 +101,7 @@ + !$OMP END CRITICAL + IF (idg.GT.0.AND.normab.GT.thresh) THEN + ! c(:,:,ig)=c(:,:,ig)+MATMUL(a(:,:,igp),b(:,:,idg)) +- CALL DGEMM_MKL95(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) ++ CALL DGEMM(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) + !$OMP CRITICAL + imul=imul+1 + !$OMP END CRITICAL +@@ -118,7 +118,7 @@ + END FUNCTION periodic_matmul + + FUNCTION periodic_matvecmul(a,b) RESULT(c) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:,:), INTENT(in) :: a + REAL*8,DIMENSION(:,:), INTENT(IN) :: b +@@ -165,7 +165,7 @@ + IF (idg.GT.0) THEN + !WRITE(6,*)'non zero matrix',idg,indexg(:,idg) + c(:,ig)=c(:,ig)+MATMUL(a(:,:,idg),b(:,igp)) +- !CALL DGEMM_MKL95(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) ++ !CALL DGEMM(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) + imul=imul+1 + ENDIF + +diff -ru periodic_nbo.orig/pre_nao.f90 periodic_nbo/pre_nao.f90 +--- periodic_nbo.orig/pre_nao.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/pre_nao.f90 2016-05-12 10:18:03.939451000 +0200 +@@ -1,5 +1,5 @@ + MODULE pre_nao +- USE MKL95_BLAS ++ USE BLAS95 + PRIVATE + PUBLIC :: do_pre_nao + +@@ -18,7 +18,7 @@ + USE matutil + USE periodic_matutil + USE nbo_shared +- USE mkl95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + + TYPE(nbo_input) :: inp +@@ -135,9 +135,9 @@ + num_elec = 0.d0 + DO ispin=1,nspins + DO ik=1,nk +- CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),energy_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),energy_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + energy_sum = energy_sum + inp%kpt_wt(ik)*mattrace(energy_test) +- !CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),sk(:,:,ik),elec_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ !CALL ZGEMM(inp%rhok(:,:,ik,ispin),sk(:,:,ik),elec_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + num_elec = num_elec + inp%kpt_wt(ik)*mattrace(inp%rhok(:,:,ik,ispin)) !sk should be the identity matrix now + ENDDO + ENDDO +@@ -193,8 +193,8 @@ + !$OMP PARALLEL DEFAULT(PRIVATE) SHARED(nk,rhok,sk) + !$OMP DO SCHEDULE(STATIC) + DO ik=1,nk +- CALL ZGEMM_MKL95(rhok(:,:,ik),sk(:,:,ik),dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL zGEMM_MKL95(sk(:,:,ik),dummy,rhok(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(rhok(:,:,ik),sk(:,:,ik),dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL zGEMM(sk(:,:,ik),dummy,rhok(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + ENDDO + !$OMP END DO NOWAIT + !$OMP END PARALLEL +@@ -298,7 +298,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),TRANSPOSE(N)) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),TRANSPOSE(N)) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(N,dummy,idenk(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(N,dummy,idenk(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) + ENDDO + !$OMP END DO NOWAIT + !$OMP END PARALLEL +@@ -365,7 +365,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Os) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Os) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Step 3c: Restoration of natural character of NRB + !(Omitted; doesn't seem important at all) +@@ -451,7 +451,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Ow) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Ow) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !WRITE(6,*)'hi occ ryd orthog' + +@@ -461,7 +461,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Ow) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Ow) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Finally with the low occupancy NRB + !Here we first do a Gram-Schmidt orthogonalization of the low occupancy states to the remainder +@@ -469,7 +469,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Os) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Os) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !WRITE(6,*)'lo occ ryd orthog' + +@@ -480,7 +480,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Ow) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Ow) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Now restore the expected order of the basis functions + sk(:,:,ik)=remap_matrix(sk(:,:,ik),irydbasisremap,.TRUE.) +@@ -656,7 +656,7 @@ + !onto the remaining basis function n+1:nbasis + Sinv=matinv(S(1:n,1:n)) + !proj=MATMUL(Sinv,S(1:n,n+1:nbasis)) +- CALL ZGEMM_MKL95(Sinv,S(1:n,n+1:nbasis),proj,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Sinv,S(1:n,n+1:nbasis),proj,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Now do gs orthogonalization using those projections + Os=0.d0 +@@ -707,7 +707,7 @@ + nbasis=SIZE(N,1) + IF (PRESENT(S)) THEN + !overlap=MATMUL(matsqrt(S),N) +- CALL DGEMM_MKL95(matsqrt(S),N,overlap,'N','N',1.d0,0.d0) ++ CALL DGEMM(matsqrt(S),N,overlap,'N','N',1.d0,0.d0) + ELSE + overlap=N + ENDIF diff --git a/easybuild/easyconfigs/n/NBO/NBO.eb b/easybuild/easyconfigs/n/NBO/NBO.eb new file mode 100644 index 0000000000..c629f66838 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'NBO' +version = '1.1' + +homepage = 'http://schmidt.chem.wisc.edu/nbosoftware' +description = """Generalized Natural Bond Orbital algorithm to handle systems characterized by periodic symmetry.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://schmidt.chem.wisc.edu/sites/schmidt.chem.wisc.edu/files/'] +sources = ['periodic_nbo_v.%(version)s.tgz'] + +patches = ['NBO-%(version)s_MKL95.patch'] + +buildopts = 'FC="$FC" LD="$FC" FFLAGS="$FFLAGS -I$LAPACK_INC_DIR/intel64/ilp64" ' +buildopts += 'LDFLAGS="$FFLAGS $LDFLAGS $LIBLAPACK -lmkl_blas95_ilp64 -lmkl_lapack95_ilp64"' + +files_to_copy = [(['nbo.exe'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/nbo.exe'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From e6233dc104ac2488f8a7ea35ec3f5df51f8de4c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 11:10:16 +0200 Subject: [PATCH 721/722] fix filename of NBO easyconfig --- easybuild/easyconfigs/n/NBO/{NBO.eb => NBO-1.1-intel-2016a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/n/NBO/{NBO.eb => NBO-1.1-intel-2016a.eb} (100%) diff --git a/easybuild/easyconfigs/n/NBO/NBO.eb b/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb similarity index 100% rename from easybuild/easyconfigs/n/NBO/NBO.eb rename to easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb -- GitLab From daf6705c34074fd88288abd68b8d470ffb390e3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 14:29:59 +0200 Subject: [PATCH 722/722] also build projection.exe tool in NBO easyconfig --- .../easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb | 18 +- .../n/NBO/projection-1.1.2_MKL95.patch | 212 ++++++++++++++++++ 2 files changed, 226 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch diff --git a/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb b/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb index c629f66838..a0ff978b52 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb @@ -10,17 +10,27 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'openmp': True} source_urls = ['http://schmidt.chem.wisc.edu/sites/schmidt.chem.wisc.edu/files/'] -sources = ['periodic_nbo_v.%(version)s.tgz'] +sources = [ + 'periodic_nbo_v.%(version)s.tgz', + 'projection_v.1.1.2.tgz', +] -patches = ['NBO-%(version)s_MKL95.patch'] +patches = [ + 'NBO-%(version)s_MKL95.patch', + ('projection-1.1.2_MKL95.patch', '..'), +] + +prebuildopts = "cd %(builddir)s/projection && " +prebuildopts += 'make FFLAGS="$FFLAGS -I$LAPACK_INC_DIR/intel64/ilp64" && ' +prebuildopts += "cd %(builddir)s/periodic_nbo && " buildopts = 'FC="$FC" LD="$FC" FFLAGS="$FFLAGS -I$LAPACK_INC_DIR/intel64/ilp64" ' buildopts += 'LDFLAGS="$FFLAGS $LDFLAGS $LIBLAPACK -lmkl_blas95_ilp64 -lmkl_lapack95_ilp64"' -files_to_copy = [(['nbo.exe'], 'bin')] +files_to_copy = [(['%(builddir)s/periodic_nbo/nbo.exe', '%(builddir)s/projection/projection.exe'], 'bin')] sanity_check_paths = { - 'files': ['bin/nbo.exe'], + 'files': ['bin/nbo.exe', 'bin/projection.exe'], 'dirs': [], } diff --git a/easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch b/easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch new file mode 100644 index 0000000000..f12e3ac7a4 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch @@ -0,0 +1,212 @@ +fix using BLAS95/LAPACK95 interface for recent Intel MKL versions +author: Kenneth Hoste (HPC-UGent) +diff -ru projection.orig/bloch_overlap.f90 projection/bloch_overlap.f90 +--- projection.orig/bloch_overlap.f90 2015-04-15 18:05:39.000000000 +0200 ++++ projection/bloch_overlap.f90 2016-05-12 13:58:53.000000000 +0200 +@@ -18,8 +18,8 @@ + ! Kudin and Scuseria, Chem. Phys. Lett.; 289, 611-616 (1998) + + SUBROUTINE bloch_space_overlap(AO_basis,index_l) +- USE mkl95_lapack +- USE mkl95_blas ++ USE LAPACK95 ++ USE BLAS95 + IMPLICIT NONE + + TYPE(AO_function), DIMENSION(:) :: AO_basis +@@ -189,9 +189,9 @@ + bloch_s_inv(:,:,ik) = bloch_s_mat(:,:,ik) + IF( SVD )THEN + !SVD inversion method, more robust but slow +- CALL ZGESVD_MKL95(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,work_array,'A') ++ CALL ZGESVD(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,work_array,'A') + !Previously used SVD routine, has numerical instability wrt really small values +- !CALL ZGESDD_MKL95(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,'A') ++ !CALL ZGESDD(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,'A') + + !This loop is the equivalent of multiplying the inverse of the singular values matrix by adjoint of the u matrix + DO j=1,s_dim +@@ -202,16 +202,16 @@ + inv_dummy(j,:) = 0.d0 + ENDIF + ENDDO +- CALL ZGEMM_MKL95(v_matrix,inv_dummy,bloch_s_inv(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(v_matrix,inv_dummy,bloch_s_inv(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) + ELSE + !LU decompostion inversion method, fast but easily suffers from instability due to linear dependency +- CALL ZGETRF_MKL95(bloch_s_inv(:,:,ik),IPIV,INFO) ++ CALL ZGETRF(bloch_s_inv(:,:,ik),IPIV,INFO) + IF( INFO /= 0 )THEN + WRITE(6,*)'The inverese of the overlap matrix for kpt',ik,'could not be computed' + WRITE(6,*)'INFO value output from ZGETRF',INFO + STOP + ENDIF +- CALL ZGETRI_MKL95(bloch_s_inv(:,:,ik),IPIV) ++ CALL ZGETRI(bloch_s_inv(:,:,ik),IPIV) + ENDIF + + !WRITE(6,*)'inverse for kpoint',ik +@@ -248,7 +248,7 @@ + !IF there are linear dependencies the best bet is to just 'trim' the basis set of its most diffuse functions. + !In periodic systems there is no 'edge' and these diffuse functions are largely uneccessary. + SUBROUTINE check_linear_depend(input_mat,eig_min) +- USE mkl95_lapack ++ USE LAPACK95 + IMPLICIT NONE + + COMPLEX*16,DIMENSION(:,:),INTENT(IN) :: input_mat +@@ -262,7 +262,7 @@ + + test_mat = input_mat + +- CALL ZHEEV_MKL95(test_mat,eigval,'V','U',INFO) ++ CALL ZHEEV(test_mat,eigval,'V','U',INFO) + + IF( INFO .NE. 0 )THEN + WRITE(6,*)'Calculating eigenvalues in check_linear_depend failed' +diff -ru projection.orig/projection_main.f90 projection/projection_main.f90 +--- projection.orig/projection_main.f90 2015-03-04 17:07:27.000000000 +0100 ++++ projection/projection_main.f90 2016-05-12 13:58:57.000000000 +0200 +@@ -4,7 +4,7 @@ + USE rd_basis + USE bloch_overlap + USE PAW +- USE mkl95_blas ++ USE BLAS95 + IMPLICIT NONE + + CHARACTER(128) :: basis_fn, VASP_fn, NBO_fn +@@ -145,28 +145,28 @@ + !Then for each basis function, nu, the contribution of the planewaves is calculated for all bands at one using vector-matrix multiplication + DO ispin=1,nspins + !each computation is SUM(nu) S-1{mu,nu} * (SUM(g) *c(a,g)) +- CALL ZGEMV_MKL95(pw_coeff(:,:,ik,ispin),AO_PW_overlap(:,ik),proj_matrix(nu,:,ik,ispin),(1.d0,0.d0),(0.d0,0.d0),'T') ++ CALL ZGEMV(pw_coeff(:,:,ik,ispin),AO_PW_overlap(:,ik),proj_matrix(nu,:,ik,ispin),(1.d0,0.d0),(0.d0,0.d0),'T') + ENDDO + ENDDO + + DO ispin=1,nspins + ! !Calculation of planewave contributions to band coeff's are done at once using matrix multiplication + ! !each computation is SUM(nu) S-1{mu,nu} * (SUM(g) *c(a,g)) +-! CALL ZGEMM_MKL95(AO_PW_overlap(:,:,ik),pw_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++! CALL ZGEMM(AO_PW_overlap(:,:,ik),pw_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + ! + ! !Since band is simply summation of PW AND PAW, PAW contirbution is simply added to PW's +-! IF( PAW_pseudo ) CALL ZGEMM_MKL95(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(1.d0,0.d0)) ++! IF( PAW_pseudo ) CALL ZGEMM(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(1.d0,0.d0)) + ! + ! !Band overlaps are finally multiplied by inverse of overlap matrix to complete projection + ! !The use of the inverse of the overlap matrix is necessary due to the non-orthogonality of the AO-basis +-! CALL ZGEMM_MKL95(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++! CALL ZGEMM(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Since band is simply summation of PW AND PAW, PAW contirbution is simply added to PW's +- IF( PAW_pseudo ) CALL ZGEMM_MKL95(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik,ispin),'N','N',(1.d0,0.d0),(1.d0,0.d0)) ++ IF( PAW_pseudo ) CALL ZGEMM(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik,ispin),'N','N',(1.d0,0.d0),(1.d0,0.d0)) + + !Band overlaps are finally multiplied by inverse of overlap matrix to complete projection + !The use of the inverse of the overlap matrix is necessary due to the non-orthogonality of the AO-basis +- CALL ZGEMM_MKL95(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik,ispin),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik,ispin),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + ENDDO + +@@ -208,19 +208,19 @@ + coeff_dummy(:,iband) = bloch_band_coeff(:,iband,ik,ispin) * weight(iband,ik,ispin) + ENDDO + !Matrix muliplication is used to calculate the density matrix +- CALL ZGEMM_MKL95(coeff_dummy,bloch_band_coeff(:,:,ik,ispin),bloch_density(:,:,ik,ispin),'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(coeff_dummy,bloch_band_coeff(:,:,ik,ispin),bloch_density(:,:,ik,ispin),'N','C',(1.d0,0.d0),(0.d0,0.d0)) + + !FOCK MATRIX + !Matrix multiplication is used to convert the Fock matrix into the projected basis + ! F{mu,nu} = SUM(fock_coeff{nu,iband}*F{iband,iband}*CONJG(fock_coeff{nu,iband})) + !First the nonorthogonality of the bloch orbtials must be addressed since the MO->AO transform is not unitary + !coeff's must be multiplied by Overlap matrix +- CALL ZGEMM_MKL95(bloch_s_mat(:,:,ik),bloch_band_coeff(:,:,ik,ispin),coeff_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_s_mat(:,:,ik),bloch_band_coeff(:,:,ik,ispin),coeff_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + !Then the trnsformation is simply a unitary transform using the new coefficients + DO iband=1,nbands + fock_dummy(iband,:) = eig(iband,ik,ispin)*CONJG(coeff_dummy(:,iband)) + ENDDO +- CALL ZGEMM_MKL95(coeff_dummy,fock_dummy,bloch_fock(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(coeff_dummy,fock_dummy,bloch_fock(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + ENDDO + ENDDO + +@@ -235,12 +235,12 @@ + energy_sum = 0.d0 + DO ispin=1,nspins + DO ik=1,nkpts +- CALL ZGEMM_MKL95(bloch_density(:,:,ik,ispin),bloch_s_mat(:,:,ik),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_density(:,:,ik,ispin),bloch_s_mat(:,:,ik),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + n_elec_dummy = n_elec_dummy*kpt_wt(ik) + DO nu=1,s_dim + num_elec = num_elec + n_elec_dummy(nu,nu) + ENDDO +- CALL ZGEMM_MKL95(bloch_density(:,:,ik,ispin),bloch_fock(:,:,ik,ispin),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_density(:,:,ik,ispin),bloch_fock(:,:,ik,ispin),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + n_elec_dummy = n_elec_dummy*kpt_wt(ik) + DO nu=1,s_dim + energy_sum = energy_sum + n_elec_dummy(nu,nu) +@@ -271,7 +271,7 @@ + !This subrotuine computes the overlap matrices of the projected bands in the AO basis. + !This information is also used to calculate the spillover (quantify how much of band density is lost in projection + SUBROUTINE calc_spillover(r_mat,band_coeff) +- USE mkl95_blas ++ USE BLAS95 + USE rd_wavefunction + USE projection_shared + IMPLICIT NONE +@@ -345,8 +345,8 @@ + + !Overlap of projected bands is computed using matrix mulitplication + !Each overlap is equal to SUM(mu) SUM(nu) c*S{mu,nu}c +- CALL ZGEMM_MKL95(bloch_s_mat(:,:,ik),band_coeff(:,:,ik,ispin),r_mat_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(band_coeff(:,:,ik,ispin),r_mat_dummy,r_mat(:,:,ik,ispin),'C','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_s_mat(:,:,ik),band_coeff(:,:,ik,ispin),r_mat_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(band_coeff(:,:,ik,ispin),r_mat_dummy,r_mat(:,:,ik,ispin),'C','N',(1.d0,0.d0),(0.d0,0.d0)) + + + !Then the norm of each band at each k-point is analyzed to make sure the norm is appropriate +diff -ru projection.orig/projection_shared.f90 projection/projection_shared.f90 +--- projection.orig/projection_shared.f90 2015-04-15 17:50:44.000000000 +0200 ++++ projection/projection_shared.f90 2016-05-12 13:59:00.000000000 +0200 +@@ -94,8 +94,8 @@ + !The bands are in the same original AO basis + !The orhtogonalizing matrix is constructed as W(WSW)^-1/2, where S is the 'overlap_mat' and W is a diagonal matrix containing the occupancy of each band + SUBROUTINE do_OWSO(overlap_mat,band_occ,band_coeff) +- USE mkl95_BLAS +- USE mkl95_LAPACK ++ USE BLAS95 ++ USE LAPACK95 + IMPLICIT NONE + + COMPLEX*16,DIMENSION(:,:),INTENT(IN) :: overlap_mat !Input overlap matrix, used to construct orthogonalizing matrix +@@ -145,7 +145,7 @@ + + !Now obtain the eigenvectors to obtain the square root matrix + eigvec = sym_weight +- CALL ZHEEV_MKL95(eigvec,eigval,'V','U',INFO) ++ CALL ZHEEV(eigvec,eigval,'V','U',INFO) + IF( INFO /= 0 )THEN + WRITE(6,*)'The eigenvalues of the overlap matrix could not be computed' + WRITE(6,*)'INFO on exit of ZHEEV',INFO +@@ -156,7 +156,7 @@ + DO iband=1,nbands + sym_weight(iband,:) = CONJG(eigvec(:,iband)) / SQRT(eigval(iband)) !Sym_weight is now just a dummy matrix for use in the BLAS routine + ENDDO +- CALL ZGEMM_MKL95(eigvec,sym_weight,sqrt_inv,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(eigvec,sym_weight,sqrt_inv,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + + !To obtain the orthogonlaizing matrix an additional multiplication by the weight matrix must be applied from the left +@@ -168,7 +168,7 @@ + !Now the bands can finally be orhtogonalized + !Note that the original coefficients are lost. They are currently unused but this will have to be rewritten if they become necessary. + coeff_dummy = band_coeff +- CALL ZGEMM_MKL95(coeff_dummy,sqrt_inv,band_coeff,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(coeff_dummy,sqrt_inv,band_coeff,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + + -- GitLab