From 05f51c46ddfcc0c854a49323bac234aa65051281 Mon Sep 17 00:00:00 2001 From: 健美猫 Date: Thu, 3 May 2018 23:08:48 +0800 Subject: Bump gatk version to 4.0.4.0. (#7985) * Bump gatk version to 4.0.4.0. * Update. * Fixed. * Fixed. --- var/spack/repos/builtin/packages/gatk/package.py | 18 +++++++++++++----- 1 file 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") -- cgit v1.2.3-70-g09d2