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gatk: new version (#9202)

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* gatk: added 4.0.8.1, fixed binary install
* gatk: fix flake8 conflict
* gatk: improve comments and modify install
This commit is contained in:
Justin Stanley 2018-09-14 15:55:52 -05:00 committed by Todd Gamblin
parent 451328d6e6
commit ff6b9b99fa
1 changed files with 5 additions and 3 deletions
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8
var/spack/repos/builtin/packages/gatk/package.py
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@ -35,6 +35,8 @@ class Gatk(Package):
homepage = "https://software.broadinstitute.org/gatk/" homepage = "https://software.broadinstitute.org/gatk/"
url = "https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip" url = "https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip"
version('4.0.8.1', sha256='6d47463dfd8c16ffae82fd29e4e73503e5b7cd0fcc6fea2ed50ee3760dd9acd9',
url='https://github.com/broadinstitute/gatk/archive/4.0.8.1.tar.gz')
version('4.0.4.0', '083d655883fb251e837eb2458141fc2b', version('4.0.4.0', '083d655883fb251e837eb2458141fc2b',
url="https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip") url="https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip")
version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz', version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
@ -46,10 +48,10 @@ class Gatk(Package):
def install(self, spec, prefix): def install(self, spec, prefix):
mkdirp(prefix.bin) mkdirp(prefix.bin)
# The list of files to install varies with release...
# ... but skip the spack-{build.env}.out files and gatkdoc directory. # Install all executable non-script files to prefix bin
files = [x for x in glob.glob("*") files = [x for x in glob.glob("*")
if not re.match("^spack-", x) and not re.match("^gatkdoc", x)] if not re.match("^.*\.sh$", x) and is_exe(x)]
for f in files: for f in files:
install(f, prefix.bin) install(f, prefix.bin)