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-rw-r--r--var/spack/repos/builtin/packages/picard/package.py75
-rw-r--r--var/spack/repos/builtin/packages/picard/picard.sh3
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 "$@"