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| author | Miles Perry <37849532+Miles-Perry@users.noreply.github.com> | 2018-11-26 11:30:21 -0600 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2018-11-26 11:30:21 -0600 |
| commit | 28e93a7a79842d37113afa9a1ff5d204dbc8d3d2 (patch) | |
| tree | 7cc772ce78751aecacbf6cd16cbcddb44c91e04a | |
| parent | 06dcf72f142cf2637a3044aae7c5bff429a9e7b4 (diff) | |
| download | spack-28e93a7a79842d37113afa9a1ff5d204dbc8d3d2.tar.gz spack-28e93a7a79842d37113afa9a1ff5d204dbc8d3d2.tar.bz2 spack-28e93a7a79842d37113afa9a1ff5d204dbc8d3d2.tar.xz spack-28e93a7a79842d37113afa9a1ff5d204dbc8d3d2.zip | |
Feature/gatk (#9872)
* added 3.8-1 version
* fixed flake8 stuff
| -rw-r--r-- | var/spack/repos/builtin/packages/gatk/package.py | 10 |
1 files changed, 4 insertions, 6 deletions
diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py index 32bb771530..23570bfd72 100644 --- a/var/spack/repos/builtin/packages/gatk/package.py +++ b/var/spack/repos/builtin/packages/gatk/package.py @@ -4,9 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * -import glob import os.path -import re class Gatk(Package): @@ -20,6 +18,8 @@ class Gatk(Package): url='https://github.com/broadinstitute/gatk/archive/4.0.8.1.tar.gz') version('4.0.4.0', '083d655883fb251e837eb2458141fc2b', url="https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip") + version('3.8-1', 'a0829534d2d0ca3ebfbd3b524a9b50427ff238e0db400d6e9e479242d98cbe5c', extension='tar.bz2', + url="https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef") version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz', url="https://software.broadinstitute.org/gatk/download/auth?package=GATK") @@ -31,10 +31,8 @@ class Gatk(Package): mkdirp(prefix.bin) # Install all executable non-script files to prefix bin - files = [x for x in glob.glob("*") - if not re.match("^.*\.sh$", x) and is_exe(x)] - for f in files: - install(f, prefix.bin) + jar_file = 'GenomeAnalysisTK.jar' + install(jar_file, prefix.bin) # Skip helper script settings if spec.satisfies('@:4.0'): |