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authorMiles Perry <37849532+Miles-Perry@users.noreply.github.com>2018-11-26 11:30:21 -0600
committerAdam J. Stewart <ajstewart426@gmail.com>2018-11-26 11:30:21 -0600
commit28e93a7a79842d37113afa9a1ff5d204dbc8d3d2 (patch)
tree7cc772ce78751aecacbf6cd16cbcddb44c91e04a
parent06dcf72f142cf2637a3044aae7c5bff429a9e7b4 (diff)
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Feature/gatk (#9872)
* added 3.8-1 version * fixed flake8 stuff
-rw-r--r--var/spack/repos/builtin/packages/gatk/package.py10
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'):