transdecoder: new package (#4895)

* transdecoder: new package

* fixed package structure

1 files changed, 50 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/transdecoder/package.py b/var/spack/repos/builtin/packages/transdecoder/package.py
new file mode 100644
index 0000000000..4c23afbf2a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/transdecoder/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# 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 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 *
+
+
+class Transdecoder(MakefilePackage):
+    """TransDecoder identifies candidate coding regions within transcript
+       sequences, such as those generated by de novo RNA-Seq transcript
+       assembly using Trinity, or constructed based on RNA-Seq alignments to
+       the genome using Tophat and Cufflinks."""
+
+    homepage = "http://transdecoder.github.io/"
+    url      = "https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz"
+
+    version('3.0.1', 'f62b86a15fcb78b1dada9f80cc25f300')
+
+    depends_on('perl', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('TransDecoder.LongOrfs', prefix)
+        install('TransDecoder.Predict', prefix)
+        install_tree('PerlLib', prefix.PerlLib)
+        install_tree('util', prefix.util)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', prefix.util.bin)
+        run_env.prepend_path('PATH', prefix)