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breakdancer: fix several issues (#9251)

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* add perl dependencies
* put bam2cfg in path
* fix perl dir
This commit is contained in:
Levi Baber 2018-09-14 22:11:34 -05:00 committed by Todd Gamblin
parent 301643bdc4
commit 3f9fc0f765
1 changed files with 29 additions and 4 deletions
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33
var/spack/repos/builtin/packages/breakdancer/package.py
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@ -26,8 +26,8 @@
class Breakdancer(CMakePackage): class Breakdancer(CMakePackage):
"""BreakDancer-1.3.6, released under GPLv3, is a Cpp package that provides """BreakDancer-1.3.6, released under GPLv3, is a perl/Cpp package that
genome-wide detection of structural variants from next generation provides genome-wide detection of structural variants from next generation
paired-end sequencing reads. It includes two complementary programs. paired-end sequencing reads. It includes two complementary programs.
BreakDancerMax predicts five types of structural variants: insertions, BreakDancerMax predicts five types of structural variants: insertions,
deletions, inversions, inter- and intra-chromosomal translocations from deletions, inversions, inter- and intra-chromosomal translocations from
@ -37,10 +37,35 @@ class Breakdancer(CMakePackage):
100bp) using normally mapped read pairs..""" 100bp) using normally mapped read pairs.."""
homepage = "http://gmt.genome.wustl.edu/packages/breakdancer" homepage = "http://gmt.genome.wustl.edu/packages/breakdancer"
git = "https://github.com/genome/breakdancer.git" url = "https://github.com/genome/breakdancer/archive/v1.4.5.tar.gz"
version('master', submodules='true') version('1.4.5', sha256='5d74f3a90f5c69026ebb4cf4cb9ccc51ec8dd49ac7a88595a1efabd5a73e92b6')
version('master', submodules='true',
git='https://github.com/genome/breakdancer.git', preferred=True)
phases = ['edit', 'cmake', 'build', 'install']
depends_on('zlib') depends_on('zlib')
depends_on('perl-statistics-descriptive', type='run')
depends_on('perl-math-cdf', type='run')
depends_on('perl-gd-graph', type='run')
depends_on('perl-gdgraph-histogram', type='run')
depends_on('perl-list-moreutils', type='run')
depends_on('perl-exporter-tiny', type='run')
# TODO: remove git submodules, and depend on boost & samtools
parallel = False parallel = False
def setup_environment(self, spack_env, run_env):
# get the perl tools in the path
run_env.prepend_path('PATH', self.prefix.lib)
def edit(self, spec, prefix):
# perl tools end up in a silly lib subdirectory, fixing that
filter_file(r'set\(SUPPORT_LIBDIR lib\/breakdancer-max\$ \
\{EXE_VERSION_SUFFIX\}\)',
'set(SUPPORT_LIBDIR lib)',
join_path(self.stage.source_path,
'perl', 'CMakeLists.txt'))