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| author | Carlos Bederián <zzzoom@gmail.com> | 2017-10-12 13:08:31 -0300 |
|---|---|---|
| committer | Christoph Junghans <christoph.junghans@gmail.com> | 2017-10-12 10:08:31 -0600 |
| commit | db149876a42ec4cc8db9e488d90d71c7d811a7a6 (patch) | |
| tree | f380e368c50f266fa1f2125f2a30db5783e7c750 | |
| parent | 87c65fafa989b27381bc78addf8e375730217e8a (diff) | |
| download | spack-db149876a42ec4cc8db9e488d90d71c7d811a7a6.tar.gz spack-db149876a42ec4cc8db9e488d90d71c7d811a7a6.tar.bz2 spack-db149876a42ec4cc8db9e488d90d71c7d811a7a6.tar.xz spack-db149876a42ec4cc8db9e488d90d71c7d811a7a6.zip | |
samtools: add version 1.6 + some fixes (#5715)
* htslib: add version 1.6
* samtools: add version 1.6, remove zlib dependency
* bcftools: add version 1.6, switch to using standalone htslib
| -rw-r--r-- | var/spack/repos/builtin/packages/bcftools/package.py | 8 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/htslib/package.py | 3 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/samtools/package.py | 9 |
3 files changed, 11 insertions, 9 deletions
diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py index 2add3e781a..cbc33b1004 100644 --- a/var/spack/repos/builtin/packages/bcftools/package.py +++ b/var/spack/repos/builtin/packages/bcftools/package.py @@ -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") diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py index 2921aee14b..e61da166f5 100644 --- a/var/spack/repos/builtin/packages/htslib/package.py +++ b/var/spack/repos/builtin/packages/htslib/package.py @@ -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:") diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py index e7976fc224..ea1dad6952 100644 --- a/var/spack/repos/builtin/packages/samtools/package.py +++ b/var/spack/repos/builtin/packages/samtools/package.py @@ -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'): |