diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/samtools/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/samtools/package.py | 106 |
1 files changed, 55 insertions, 51 deletions
diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py index c589e42da8..c44c36008f 100644 --- a/var/spack/repos/builtin/packages/samtools/package.py +++ b/var/spack/repos/builtin/packages/samtools/package.py @@ -8,73 +8,77 @@ from spack.package import * class Samtools(Package): """SAM Tools provide various utilities for manipulating alignments in - the SAM format, including sorting, merging, indexing and generating - alignments in a per-position format""" + the SAM format, including sorting, merging, indexing and generating + alignments in a per-position format""" homepage = "https://www.htslib.org" - url = "https://github.com/samtools/samtools/releases/download/1.13/samtools-1.13.tar.bz2" + url = "https://github.com/samtools/samtools/releases/download/1.13/samtools-1.13.tar.bz2" - version('1.14', sha256='9341dabaa98b0ea7d60fd47e42af25df43a7d3d64d8e654cdf852974546b7d74') - version('1.13', sha256='616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60') - version('1.12', sha256='6da3770563b1c545ca8bdf78cf535e6d1753d6383983c7929245d5dba2902dcb') - version('1.10', sha256='7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585') - version('1.9', sha256='083f688d7070082411c72c27372104ed472ed7a620591d06f928e653ebc23482') - version('1.8', sha256='c942bc1d9b85fd1b05ea79c5afd2805d489cd36b2c2d8517462682a4d779be16') - version('1.7', sha256='e7b09673176aa32937abd80f95f432809e722f141b5342186dfef6a53df64ca1') - version('1.6', sha256='ee5cd2c8d158a5969a6db59195ff90923c662000816cc0c41a190b2964dbe49e') - version('1.5', sha256='8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6') - version('1.4', sha256='9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4') - version('1.3.1', sha256='6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e') - version('1.2', sha256='420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa') - version('0.1.8', sha256='343daf96f035c499c5b82dce7b4d96b10473308277e40c435942b6449853815b', - url="https://github.com/samtools/samtools/archive/0.1.8.tar.gz") + version("1.14", sha256="9341dabaa98b0ea7d60fd47e42af25df43a7d3d64d8e654cdf852974546b7d74") + version("1.13", sha256="616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60") + version("1.12", sha256="6da3770563b1c545ca8bdf78cf535e6d1753d6383983c7929245d5dba2902dcb") + version("1.10", sha256="7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585") + version("1.9", sha256="083f688d7070082411c72c27372104ed472ed7a620591d06f928e653ebc23482") + version("1.8", sha256="c942bc1d9b85fd1b05ea79c5afd2805d489cd36b2c2d8517462682a4d779be16") + version("1.7", sha256="e7b09673176aa32937abd80f95f432809e722f141b5342186dfef6a53df64ca1") + version("1.6", sha256="ee5cd2c8d158a5969a6db59195ff90923c662000816cc0c41a190b2964dbe49e") + version("1.5", sha256="8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6") + version("1.4", sha256="9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4") + version("1.3.1", sha256="6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e") + version("1.2", sha256="420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa") + version( + "0.1.8", + sha256="343daf96f035c499c5b82dce7b4d96b10473308277e40c435942b6449853815b", + url="https://github.com/samtools/samtools/archive/0.1.8.tar.gz", + ) - depends_on('zlib') - depends_on('ncurses') - depends_on('perl', type='run') - depends_on('python', type='run') + depends_on("zlib") + depends_on("ncurses") + depends_on("perl", type="run") + depends_on("python", type="run") # htslib became standalone @1.3.1, must use corresponding version - depends_on('htslib@1.14', when='@1.14') - depends_on('htslib@1.13', when='@1.13') - depends_on('htslib@1.12', when='@1.12') - depends_on('htslib@1.11', when='@1.11') - depends_on('htslib@1.10.2', when='@1.10') - depends_on('htslib@1.9', when='@1.9') - depends_on('htslib@1.8', when='@1.8') - depends_on('htslib@1.7', when='@1.7') - depends_on('htslib@1.6', when='@1.6') - depends_on('htslib@1.5', when='@1.5') - depends_on('htslib@1.4', when='@1.4') - depends_on('htslib@1.3.1', when='@1.3.1') + depends_on("htslib@1.14", when="@1.14") + depends_on("htslib@1.13", when="@1.13") + depends_on("htslib@1.12", when="@1.12") + depends_on("htslib@1.11", when="@1.11") + depends_on("htslib@1.10.2", when="@1.10") + depends_on("htslib@1.9", when="@1.9") + depends_on("htslib@1.8", when="@1.8") + depends_on("htslib@1.7", when="@1.7") + depends_on("htslib@1.6", when="@1.6") + depends_on("htslib@1.5", when="@1.5") + depends_on("htslib@1.4", when="@1.4") + depends_on("htslib@1.3.1", when="@1.3.1") def install(self, spec, prefix): - if '+termlib' in spec['ncurses']: - curses_lib = '-lncursesw -ltinfow' + if "+termlib" in spec["ncurses"]: + curses_lib = "-lncursesw -ltinfow" else: - curses_lib = '-lncursesw' + curses_lib = "-lncursesw" - if self.spec.version >= Version('1.3.1'): - configure('--prefix={0}'.format(prefix), - '--with-htslib={0}'.format(self.spec['htslib'].prefix), - '--with-ncurses', - 'CURSES_LIB={0}'.format(curses_lib)) + if self.spec.version >= Version("1.3.1"): + configure( + "--prefix={0}".format(prefix), + "--with-htslib={0}".format(self.spec["htslib"].prefix), + "--with-ncurses", + "CURSES_LIB={0}".format(curses_lib), + ) make() - make('install') + make("install") else: - make('prefix={0}'.format(prefix), - 'LIBCURSES={0}'.format(curses_lib)) - if self.spec.version == Version('0.1.8'): - make('prefix={0}'.format(prefix)) + make("prefix={0}".format(prefix), "LIBCURSES={0}".format(curses_lib)) + if self.spec.version == Version("0.1.8"): + make("prefix={0}".format(prefix)) else: - make('prefix={0}'.format(prefix), 'install') + make("prefix={0}".format(prefix), "install") # Install dev headers and libs for legacy apps depending on them # per https://github.com/samtools/samtools/releases/tag/1.14 # these have been removed (bam.h still exists but paired down) - if spec.satisfies('@:1.13'): + if spec.satisfies("@:1.13"): mkdir(prefix.include) mkdir(prefix.lib) - install('sam.h', prefix.include) - install('bam.h', prefix.include) - install('libbam.a', prefix.lib) + install("sam.h", prefix.include) + install("bam.h", prefix.include) + install("libbam.a", prefix.lib) |