diff options
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/samtools/package.py | 37 |
1 files changed, 25 insertions, 12 deletions
diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py index 0becd0104b..ad1eb5e38d 100644 --- a/var/spack/repos/builtin/packages/samtools/package.py +++ b/var/spack/repos/builtin/packages/samtools/package.py @@ -14,6 +14,7 @@ class Samtools(Package): homepage = "www.htslib.org" url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" + version('1.10', sha256='7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585') version('1.9', sha256='083f688d7070082411c72c27372104ed472ed7a620591d06f928e653ebc23482') version('1.8', sha256='c942bc1d9b85fd1b05ea79c5afd2805d489cd36b2c2d8517462682a4d779be16') version('1.7', sha256='e7b09673176aa32937abd80f95f432809e722f141b5342186dfef6a53df64ca1') @@ -23,27 +24,39 @@ class Samtools(Package): version('1.3.1', sha256='6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e') version('1.2', sha256='420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa') + 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@1.9', 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@1.10.2', 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('zlib') - depends_on('bzip2') def install(self, spec, prefix): + if '+termlib' in spec['ncurses']: + curses_lib = '-lncursesw -ltinfow' + else: + curses_lib = '-lncursesw' + if self.spec.version >= Version('1.3.1'): - configure('--prefix={0}'.format(prefix), '--with-ncurses', - 'CURSES_LIB=-lncursesw') + configure('--prefix={0}'.format(prefix), + '--with-htslib={0}'.format(self.spec['htslib'].prefix), + '--with-ncurses', + 'CURSES_LIB={0}'.format(curses_lib)) make() make('install') else: - make("prefix=%s" % prefix) - make("prefix=%s" % prefix, "install") + make('prefix={0}'.format(prefix), + 'LIBCURSES={0}'.format(curses_lib)) + make('prefix={0}'.format(prefix), 'install') + # Install dev headers and libs for legacy apps depending on them mkdir(prefix.include) mkdir(prefix.lib) |