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Bump gatk version to 4.0.4.0. (#7985)

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* Bump gatk version to 4.0.4.0.

* Update.

* Fixed.

* Fixed.
This commit is contained in:
健美猫 2018-05-03 23:08:48 +08:00 committed by Adam J. Stewart
parent fb9898230e
commit 05f51c46dd
1 changed files with 13 additions and 5 deletions
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18
var/spack/repos/builtin/packages/gatk/package.py
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@ -33,23 +33,31 @@ class Gatk(Package):
"""Genome Analysis Toolkit
Variant Discovery in High-Throughput Sequencing Data
"""
homepage = "http://broadinstitute.github.io/gatk/"
url = "https://software.broadinstitute.org/gatk/download/auth?package=GATK"
_urlfmt = "https://github.com/broadgsa/gatk-protected/archive/{0}.tar.gz"
homepage = "https://software.broadinstitute.org/gatk/"
url = "https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip"
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('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
url="https://software.broadinstitute.org/gatk/download/auth?package=GATK")
depends_on('java@8:', type='run')
depends_on('python@2.6:2.8,3.6:', type='run', when='@4.0:')
depends_on('r@3.2:', type='run', when='@4.0:')
def install(self, spec, prefix):
mkdirp(prefix.bin)
# The list of files to install varies with release...
# ... but skip the spack-{build.env}.out files.
files = [x for x in glob.glob("*") if not re.match("^spack-", x)]
# ... but skip the spack-{build.env}.out files and gatkdoc directory.
files = [x for x in glob.glob("*")
if not re.match("^spack-", x) and not re.match("^gatkdoc", x)]
for f in files:
install(f, prefix.bin)
# Skip helper script settings
if spec.satisfies('@:4.0'):
return
# Set up a helper script to call java on the jar file,
# explicitly codes the path for java and the jar file.
script_sh = join_path(os.path.dirname(__file__), "gatk.sh")