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authorGeorge Hartzell <hartzell@alerce.com>2017-10-06 12:58:34 -0700
committerChristoph Junghans <christoph.junghans@gmail.com>2017-10-06 13:58:34 -0600
commita659f0f8f4672933fc36cecfe62c65366c496f07 (patch)
tree402aeeb2b54e8e8d57cf05fdf901e8e1e8226c62
parent202c66d90c9b5e41dba2c5ca51748a79b1f4d50f (diff)
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Add a package for VarDictJava@1.5.1 (#5626)
This is a simple package that drops their shell wrapper into prefix.bin and their jar files into prefix.lib. The approach comes from the picard package.
-rw-r--r--var/spack/repos/builtin/packages/vardictjava/package.py47
1 files changed, 47 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/vardictjava/package.py b/var/spack/repos/builtin/packages/vardictjava/package.py
new file mode 100644
index 0000000000..e255411acc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/vardictjava/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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 NOTICE and LICENSE files 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 *
+import glob
+
+
+class Vardictjava(Package):
+ """VarDictJava is a variant discovery program written in Java.
+ It is a partial Java port of VarDict variant caller."""
+
+ homepage = "https://github.com/AstraZeneca-NGS/VarDictJava"
+ url = "https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v1.5.1/VarDict-1.5.1.tar"
+
+ version('1.5.1', '8c0387bcc1f7dc696b04e926c48b27e6')
+
+ depends_on('java@8:', type='run')
+
+ def install(self, spec, prefix):
+ mkdirp(prefix.bin)
+ install('bin/VarDict', prefix.bin)
+
+ mkdirp(prefix.lib)
+ files = [x for x in glob.glob("lib/*jar")]
+ for f in files:
+ install(f, prefix.lib)