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| author | 健美猫 <weijianwen@gmail.com> | 2018-05-03 23:08:48 +0800 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2018-05-03 10:08:48 -0500 |
| commit | 05f51c46ddfcc0c854a49323bac234aa65051281 (patch) | |
| tree | 95d1181bd5e162783ab4c3e279494a8dd6a8a3c0 | |
| parent | fb9898230e39c973d5b570c0b146fa92fa46abd6 (diff) | |
| download | spack-05f51c46ddfcc0c854a49323bac234aa65051281.tar.gz spack-05f51c46ddfcc0c854a49323bac234aa65051281.tar.bz2 spack-05f51c46ddfcc0c854a49323bac234aa65051281.tar.xz spack-05f51c46ddfcc0c854a49323bac234aa65051281.zip | |
Bump gatk version to 4.0.4.0. (#7985)
* Bump gatk version to 4.0.4.0.
* Update.
* Fixed.
* Fixed.
| -rw-r--r-- | var/spack/repos/builtin/packages/gatk/package.py | 18 |
1 files changed, 13 insertions, 5 deletions
diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py index 8ac97bae8b..8ca12f133a 100644 --- a/var/spack/repos/builtin/packages/gatk/package.py +++ b/var/spack/repos/builtin/packages/gatk/package.py @@ -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") |