diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/breakdancer/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/breakdancer/package.py | 43 |
1 files changed, 24 insertions, 19 deletions
diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py index 53f5fed6df..e3538ea8a6 100644 --- a/var/spack/repos/builtin/packages/breakdancer/package.py +++ b/var/spack/repos/builtin/packages/breakdancer/package.py @@ -18,22 +18,26 @@ class Breakdancer(CMakePackage): 100bp) using normally mapped read pairs..""" homepage = "https://gmt.genome.wustl.edu/packages/breakdancer" - url = "https://github.com/genome/breakdancer/archive/v1.4.5.tar.gz" + url = "https://github.com/genome/breakdancer/archive/v1.4.5.tar.gz" - version('1.4.5', sha256='5d74f3a90f5c69026ebb4cf4cb9ccc51ec8dd49ac7a88595a1efabd5a73e92b6') - version('master', submodules='true', - git='https://github.com/genome/breakdancer.git', preferred=True) + version("1.4.5", sha256="5d74f3a90f5c69026ebb4cf4cb9ccc51ec8dd49ac7a88595a1efabd5a73e92b6") + version( + "master", + submodules="true", + git="https://github.com/genome/breakdancer.git", + preferred=True, + ) - depends_on('zlib') + depends_on("zlib") - depends_on('ncurses', type='link') + depends_on("ncurses", type="link") - depends_on('perl-statistics-descriptive', type='run') - depends_on('perl-math-cdf', type='run') - depends_on('perl-gdgraph', type='run') - depends_on('perl-gdgraph-histogram', type='run') - depends_on('perl-list-moreutils', type='run') - depends_on('perl-exporter-tiny', type='run') + depends_on("perl-statistics-descriptive", type="run") + depends_on("perl-math-cdf", type="run") + depends_on("perl-gdgraph", 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 @@ -41,13 +45,14 @@ class Breakdancer(CMakePackage): def setup_run_environment(self, env): # get the perl tools in the path - env.prepend_path('PATH', self.prefix.lib) + env.prepend_path("PATH", self.prefix.lib) - @run_before('cmake') + @run_before("cmake") def edit(self): # 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')) + 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"), + ) |