diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/samtools/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/samtools/package.py | 26 |
1 files changed, 17 insertions, 9 deletions
diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py index f5c7f4431f..6b0b224785 100644 --- a/var/spack/repos/builtin/packages/samtools/package.py +++ b/var/spack/repos/builtin/packages/samtools/package.py @@ -24,19 +24,27 @@ ############################################################################## from spack import * + class Samtools(Package): - """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating + """SAM Tools provide various utilities for manipulating alignments in + the SAM format, including sorting, merging, indexing and generating alignments in a per-position format""" homepage = "www.htslib.org" - version('1.2','988ec4c3058a6ceda36503eebecd4122',url = "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2") + url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" - depends_on("zlib") - depends_on("mpc") - parallel=False - patch("samtools1.2.patch",level=0) + version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88') + version('1.2', '988ec4c3058a6ceda36503eebecd4122') - def install(self, spec, prefix): - make("prefix=%s" % prefix, "install") + depends_on("ncurses") + depends_on("htslib", when='@1.3.1:') # htslib became standalone + depends_on('zlib', when='@1.2') # needed for builtin htslib + def install(self, spec, prefix): + if self.spec.version >= Version('1.3.1'): + configure('--prefix={0}'.format(prefix), '--with-ncurses') + make() + make('install') + else: + make("prefix=%s" % prefix) + make("prefix=%s" % prefix, "install") |