##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
# Authors::   Fotis Georgatos <fotis@cern.ch>
# 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 = "Bundle"

name = 'HPCBIOS_Bioinfo'
version = '20130829'

homepage = 'http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html'
description = """Bioinformatics & Computational Biology productivity environment includes a set of HPC tools,
 which are needed for scientific computing and visualization in the respective domain. """

toolchain = {'name': 'ictce', 'version': '5.3.0'}  # ie. build against the INTEL compilers & MPI stack / March 2013

dependencies = [
    #    ('ALLPATHS-LG', '46968'),
    ('AMOS', '3.1.0'),
    ('BFAST', '0.7.0a'),
    ('BLAST+', '2.2.28', '-Python-2.7.3'),
    ('BWA', '0.6.2'),
    ('BamTools', '2.2.3'),
    ('BioPerl', '1.6.1', '-Perl-5.16.3'),
    ('Biopython', '1.61', '-Python-2.7.3'),
    ('Bowtie2', '2.0.2'),
    ('bam2fastq', '1.1.0'),
    ('biodeps', '1.6'),
    ('CD-HIT', '4.5.4', '-2011-03-07'),
    ('ClustalW2', '2.1'),
    ('Cufflinks', '2.0.2'),
    ('EMBOSS', '6.5.7'),
    ('FASTA', '36.3.5e'),
    ('FASTX-Toolkit', '0.0.13.2'),
    ('FSL', '4.1.9'),
    ('GLIMMER', '3.02b'),
    ('GROMACS', '4.6.1', '-hybrid'),
    ('HMMER', '3.0'),
    #    ('HH-suite', '2.0.16'),
    ('Infernal', '1.1rc1'),
    ('libgtextutils', '0.6.1'),
    ('libharu', '2.2.0'),
    ('MCL', '12.135'),
    ('MEME', '4.8.0'),
    ('MUMmer', '3.23'),
    ('MetaVelvet', '1.2.01'),
    ('Mothur', '1.30.2'),
    ('MrBayes', '3.1.2'),
    ('mpiBLAST', '1.6.0'),
    ('NEURON', '7.2'),
    ('Oases', '0.2.08'),
    ('PAML', '4.7'),
    ('PLINK', '1.07'),
    ('Pasha', '1.0.3'),
    ('Primer3', '2.3.0'),
    ('RAxML', '7.7.5', '-hybrid-sse3'),
    ('RNAz', '2.1'),
    ('SAMtools', '0.1.18'),
    ('SHRiMP', '2.2.3'),
    ('SOAPdenovo', '1.05'),
    ('Trinity', '2012-10-05'),
    ('Velvet', '1.2.07'),
    ('ViennaRNA', '2.0.7'),
]

moduleclass = 'bio'
