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Feature/gatk (#9872)

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* added 3.8-1 version

* fixed flake8 stuff
This commit is contained in:
Miles Perry 2018-11-26 11:30:21 -06:00 committed by Adam J. Stewart
parent 06dcf72f14
commit 28e93a7a79
1 changed files with 4 additions and 6 deletions
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10
var/spack/repos/builtin/packages/gatk/package.py
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@ -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 @@ def install(self, spec, prefix):
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'):