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| -rw-r--r-- | var/spack/repos/builtin/packages/picard/package.py | 75 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/picard/picard.sh | 3 |
2 files changed, 78 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/picard/package.py b/var/spack/repos/builtin/packages/picard/package.py new file mode 100644 index 0000000000..0a52db4264 --- /dev/null +++ b/var/spack/repos/builtin/packages/picard/package.py @@ -0,0 +1,75 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +from shutil import copyfile +import glob +import os.path +import re + + +class Picard(Package): + """Picard is a set of command line tools for manipulating high-throughput + sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. + """ + + homepage = "http://broadinstitute.github.io/picard/" + url = "https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar" + + # They started distributing a single jar file at v2.6.0, prior to + # that it was a .zip file with multiple .jar and .so files + version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False, + url="https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar") + version('1.140', '308f95516d94c1f3273a4e7e2b315ec2', + url='https://github.com/broadinstitute/picard/releases/download/1.140/picard-tools-1.140.zip') + + depends_on('jdk@8:', type='run') + + 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)] + for f in files: + install(f, prefix.bin) + + # 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__), "picard.sh") + script = join_path(prefix.bin, "picard") + copyfile(script_sh, script) + set_executable(script) + + # Munge the helper script to explicitly point to java and the + # jar file. + java = join_path(self.spec['jdk'].prefix, 'bin', 'java') + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + filter_file('^java', java, script, **kwargs) + filter_file('picard.jar', join_path(prefix.bin, 'picard.jar'), + script, **kwargs) + + def setup_environment(self, spack_env, run_env): + """The Picard docs suggest setting this as a convenience.""" + run_env.prepend_path('PICARD', + join_path(self.prefix, 'bin', 'picard.jar')) diff --git a/var/spack/repos/builtin/packages/picard/picard.sh b/var/spack/repos/builtin/packages/picard/picard.sh new file mode 100644 index 0000000000..6d4864f118 --- /dev/null +++ b/var/spack/repos/builtin/packages/picard/picard.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the picard jar file +java -jar picard.jar "$@" |