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samtools: add version 1.6 + some fixes (#5715)

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* htslib: add version 1.6

* samtools: add version 1.6, remove zlib dependency

* bcftools: add version 1.6, switch to using standalone htslib
This commit is contained in:
Carlos Bederián 2017-10-12 13:08:31 -03:00 committed by Christoph Junghans
parent 87c65fafa9
commit db149876a4
3 changed files with 11 additions and 9 deletions
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8
var/spack/repos/builtin/packages/bcftools/package.py
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@ -34,13 +34,13 @@ class Bcftools(Package):
homepage = "http://samtools.github.io/bcftools/"
url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
version('1.6', 'c4dba1e8cb55db0f94b4c47724b4f9fa')
version('1.4', '50ccf0a073bd70e99cdb3c8be830416e')
version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb')
depends_on('zlib')
depends_on('bzip2', when="@1.4:")
# build fails without xz
depends_on('xz', when="@1.4")
depends_on('htslib@1.6', when='@1.6')
depends_on('htslib@1.4', when='@1.4')
depends_on('htslib@1.3.1', when='@1.3.1')
def install(self, spec, prefix):
make("prefix=%s" % prefix, "all")

3
var/spack/repos/builtin/packages/htslib/package.py
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@ -31,9 +31,10 @@ class Htslib(AutotoolsPackage):
homepage = "https://github.com/samtools/htslib"
url = "https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2"
version('1.6', 'd6fd14e208aca7e08cbe9072233d0af9')
version('1.4', '2a22ff382654c033c40e4ec3ea880050')
version('1.3.1', '16d78f90b72f29971b042e8da8be6843')
depends_on('zlib')
depends_on('bzip2', when="@1.4:")
depends_on('xz')
depends_on('xz', when="@1.4:")

9
var/spack/repos/builtin/packages/samtools/package.py
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@ -33,15 +33,16 @@ 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('1.6', 'b756f05fd5d1a7042074417edb8c9aea')
version('1.4', '8cbd7d2a0ec16d834babcd6c6d85d691')
version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88')
version('1.2', '988ec4c3058a6ceda36503eebecd4122')
depends_on("ncurses")
depends_on('ncurses')
# htslib became standalone @1.3.1, must use corresponding version
depends_on("htslib@1.4", when='@1.4')
depends_on("htslib@1.3.1", when='@1.3.1')
depends_on('zlib', when='@1.2') # needed for builtin htslib
depends_on('htslib@1.6', when='@1.6')
depends_on('htslib@1.4', when='@1.4')
depends_on('htslib@1.3.1', when='@1.3.1')
def install(self, spec, prefix):
if self.spec.version >= Version('1.3.1'):