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authorDouglas Duckworth <quackmaster@protonmail.com>2017-05-27 16:02:39 -0400
committerAdam J. Stewart <ajstewart426@gmail.com>2017-05-27 15:02:39 -0500
commitf14041d6c1902ea18d74690374074a8d0d256ffe (patch)
treea8bd49ad9dbd54a5c7b6414dafb967d0fe3520d3
parent50e729173ba49f0c95ae98266caca16b119f481a (diff)
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added STAR aligner package (#4368)
* added STAR aligner package * fixed flake errors * PATH NOW WORKS * STAR install now works * star install now perfected
-rw-r--r--var/spack/repos/builtin/packages/star/package.py41
1 files changed, 41 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/star/package.py b/var/spack/repos/builtin/packages/star/package.py
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+++ b/var/spack/repos/builtin/packages/star/package.py
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+##############################################################################
+# 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 *
+
+
+class Star(Package):
+ """STAR is an ultrafast universal RNA-seq aligner."""
+
+ homepage = "https://github.com/alexdobin/STAR"
+ url = "https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz"
+
+ version('2.5.3a', 'baf8d1b62a50482cfa13acb7652dc391')
+
+ def install(self, spec, prefix):
+ with working_dir('source'):
+ make('STAR', 'STARlong')
+ mkdirp(prefix.bin)
+ install('STAR', prefix.bin)
+ install('STARlong', prefix.bin)