diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/gatk/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/gatk/package.py | 62 |
1 files changed, 34 insertions, 28 deletions
diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py index e662b65d59..6398341606 100644 --- a/var/spack/repos/builtin/packages/gatk/package.py +++ b/var/spack/repos/builtin/packages/gatk/package.py @@ -15,31 +15,39 @@ class Gatk(Package): """ homepage = "https://gatk.broadinstitute.org/hc/en-us" - url = "https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip" + url = "https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip" list_url = "https://github.com/broadinstitute/gatk/releases" - maintainers = ['snehring'] + maintainers = ["snehring"] - version('4.2.6.1', sha256='1125cfc862301d437310506c8774d36c3a90d00d52c7b5d6b59dac7241203628') - version('4.2.2.0', sha256='ddd902441d1874493796566159288e9df178714ac18216ba05092136db1497fd') - version('4.1.8.1', sha256="42e6de5059232df1ad5785c68c39a53dc1b54afe7bb086d0129f4dc95fb182bc") - version('4.1.8.0', sha256="3ce1c2a15c44d0cfc9b2c26111f4518c215a5f9314072b4eb61f07ab5d01eef6") - version('4.1.7.0', sha256="1ed6f7c3194563a16c53b66e64d1b16d3f5e919d057d9e60f0ae6570eb0882e3") - version('4.1.6.0', sha256="1a8a0256693c0e1fb83d87b6da4bad4a182bfc2a762394650b627a882694c306") - version('4.1.5.0', sha256="6fc152c2cae0cc54c7c4cfdfd865a64f7054a820f7d02ca2549511af1dd9882b") - version('4.1.4.1', sha256="21ae694cfc8b7447381ad5ce62ed4af22e53a228b12495bdcca7df0c73b09cea") - version('4.1.4.0', sha256="ae54a2b938f704e15ea03d1822b4ce80d9a02108dc3a2b482d80b93edae3d492") - version('4.1.3.0', sha256="56fd4f03b15a8a01eaa4629f62e3ab15e4d4b957c787efd2d5629b2658c3df0a") - version('4.1.2.0', sha256="ffc5f9b3d4b35772ee5dac3060b59dc657f30e830745160671d84d732c30dc65") - version('4.1.1.0', sha256="0d997aaf5c633643c07f0e5f74d0e20364a0f1304b04355bc6e073c65fab6554") - version('4.1.0.0', sha256="148aa061328d922a570d0120d88f27e61e5da877f542206f4d77f2d788b7d21d") - version('4.0.12.0', sha256="733134303f4961dec589247ff006612b7a94171fab8913c5d44c836aa086865f") - version('4.0.11.0', sha256="5ee23159be7c65051335ac155444c6a49c4d8e3515d4227646c0686819934536") - version('4.0.8.1', sha256="e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9") - version('4.0.4.0', sha256="801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4") - version('3.8.1', sha256='a0829534d2d0ca3ebfbd3b524a9b50427ff238e0db400d6e9e479242d98cbe5c', extension="tar.bz2", - url='https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2') - version('3.8.0', sha256="d1017b851f0cc6442b75ac88dd438e58203fa3ef1d1c38eb280071ae3803b9f1", extension="tar.bz2", - url='https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2') + version("4.2.6.1", sha256="1125cfc862301d437310506c8774d36c3a90d00d52c7b5d6b59dac7241203628") + version("4.2.2.0", sha256="ddd902441d1874493796566159288e9df178714ac18216ba05092136db1497fd") + version("4.1.8.1", sha256="42e6de5059232df1ad5785c68c39a53dc1b54afe7bb086d0129f4dc95fb182bc") + version("4.1.8.0", sha256="3ce1c2a15c44d0cfc9b2c26111f4518c215a5f9314072b4eb61f07ab5d01eef6") + version("4.1.7.0", sha256="1ed6f7c3194563a16c53b66e64d1b16d3f5e919d057d9e60f0ae6570eb0882e3") + version("4.1.6.0", sha256="1a8a0256693c0e1fb83d87b6da4bad4a182bfc2a762394650b627a882694c306") + version("4.1.5.0", sha256="6fc152c2cae0cc54c7c4cfdfd865a64f7054a820f7d02ca2549511af1dd9882b") + version("4.1.4.1", sha256="21ae694cfc8b7447381ad5ce62ed4af22e53a228b12495bdcca7df0c73b09cea") + version("4.1.4.0", sha256="ae54a2b938f704e15ea03d1822b4ce80d9a02108dc3a2b482d80b93edae3d492") + version("4.1.3.0", sha256="56fd4f03b15a8a01eaa4629f62e3ab15e4d4b957c787efd2d5629b2658c3df0a") + version("4.1.2.0", sha256="ffc5f9b3d4b35772ee5dac3060b59dc657f30e830745160671d84d732c30dc65") + version("4.1.1.0", sha256="0d997aaf5c633643c07f0e5f74d0e20364a0f1304b04355bc6e073c65fab6554") + version("4.1.0.0", sha256="148aa061328d922a570d0120d88f27e61e5da877f542206f4d77f2d788b7d21d") + version("4.0.12.0", sha256="733134303f4961dec589247ff006612b7a94171fab8913c5d44c836aa086865f") + version("4.0.11.0", sha256="5ee23159be7c65051335ac155444c6a49c4d8e3515d4227646c0686819934536") + version("4.0.8.1", sha256="e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9") + version("4.0.4.0", sha256="801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4") + version( + "3.8.1", + sha256="a0829534d2d0ca3ebfbd3b524a9b50427ff238e0db400d6e9e479242d98cbe5c", + extension="tar.bz2", + url="https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2", + ) + version( + "3.8.0", + sha256="d1017b851f0cc6442b75ac88dd438e58203fa3ef1d1c38eb280071ae3803b9f1", + extension="tar.bz2", + url="https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2", + ) # Make r a variant. According to the gatk docs it is not essential and not # tested. @@ -50,7 +58,7 @@ class Gatk(Package): # R is still required by several of the unit tests. Plotting is currently # untested and should be viewed as a convenience rather than a primary # output. - variant('r', default=False, description='Use R for plotting') + variant("r", default=False, description="Use R for plotting") depends_on("java@8:", type="run") depends_on("python@2.6:2.8,3.6:", type="run", when="@4.0:") @@ -66,7 +74,7 @@ class Gatk(Package): # Skip helper script for versions >4.0 if spec.satisfies("@4.0:"): - set_executable('gatk') + set_executable("gatk") install("gatk", prefix.bin) else: # Set up a helper script to call java on the jar file, @@ -89,6 +97,4 @@ class Gatk(Package): ) def setup_run_environment(self, env): - env.prepend_path( - "GATK", join_path(self.prefix.bin, "GenomeAnalysisTK.jar") - ) + env.prepend_path("GATK", join_path(self.prefix.bin, "GenomeAnalysisTK.jar")) |