added STAR aligner package (#4368)

* added STAR aligner package

* fixed flake errors

* PATH NOW WORKS

* STAR install now works

* star install now perfected

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
new file mode 100644
index 0000000000..87c30733e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/star/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# 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)