breakdancer-1.4.5-foss-2014b.eb

# easybuild easyconfig 
#
# John Dey jfdey@fredhutch.org 
# 
# Fred Hutchenson Cancer Research Center 
#
# breakdancer uses git clone --recursive to load additional code sets outside
# of the repository.  breakdancer.tar.gz was created manualy.
#
# mkdir temp
# cd temp
# git clone --recursive https://github.com/genome/breakdancer.git
# cd breakdancer
# git checkout v1.4.5
# cd ..
# tar -czvf breakdancer-1.4.5.tar.gz --exclude .git* breakdancer/
# mkdir  $EASYBUILD_SOURCEPATH/b/breakdancer
# cp breakdancer-1.4.5.tar.gz  $EASYBUILD_SOURCEPATH/b/breakdancer
#
# toolchain 2014b was required due to dependancy with gcc
# boost 1.3 will not build with >gcc 4.8.4; 

easyblock = 'CMakeMake'

name = 'breakdancer'
version = '1.4.5'

homepage = 'http://gmt.genome.wustl.edu/packages/breakdancer/index.html'
description = """BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation."""

toolchain = {'name': 'foss', 'version': '2014b'}

source_urls = [('https://github.com/genome/breakdancer/archive')]
sources = [SOURCE_TAR_GZ]

builddependencies = [
    ('CMake', '3.0.0'),
    ('zlib', '1.2.8'),
]

dependencies = [
#   ('SAMtools', '1.3.1'),
#   ('BamTools', '2.4.1'),
#   ('HTSlib', '1.3.1'),
]

unpack_options = ' && mkdir breakdancer/build '
srcdir = '..'
start_dir = 'build'
configopts = ' .. -DCMAKE_BUILD_TYPE=release '
maxparallel = 1

sanity_check_paths = {
    'dirs': ['bin', 'lib'],
    'files': ['bin/breakdancer-max',
              'lib/breakdancer-maxunstable/AlnParser.pm',
              'lib/breakdancer-maxunstable/Poisson.pm',
              'lib/breakdancer-maxunstable/bam2cfg.pl',
              ],
}

moduleclass = 'bio'