updating gatk to 4.2.2.0

Signed-off-by: vsoch <vsoch@users.noreply.github.com>
vsoch · Sep 17, 2021 · 6ad5b94 · 6ad5b94
1 parent be8e52f
commit 6ad5b94
Showing 1 changed file with 21 additions and 73 deletions.
diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py
@@ -13,81 +13,29 @@ class Gatk(Package):
     """
 
     homepage = "https://gatk.broadinstitute.org/hc/en-us"
-    url = "https://github.com/broadinstitute/gatk/releases/download/4.1.0.0/gatk-4.1.0.0.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"
 
-    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('4.2.2.0', 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.