sspace-standard: new pacakge (#5071)

* sspace-standard: new pacakge

* fixing install versioning

* fixing description

1 files changed, 56 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/sspace-standard/package.py b/var/spack/repos/builtin/packages/sspace-standard/package.py
new file mode 100644
index 0000000000..7b1de9c1b3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sspace-standard/package.py
@@ -0,0 +1,56 @@
+##############################################################################
+# 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 *
+import os
+
+
+class SspaceStandard(Package):
+    """SSPACE standard is a stand-alone program for scaffolding pre-assembled
+       contigs using NGS paired-read data
+
+       Note: A manual download is required for SSPACE-Standard.
+       Spack will search your current directory for the download file.
+       Alternatively, add this file to a mirror so that Spack can find it.
+       For instructions on how to set up a mirror, see
+       http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE"
+    url      = "file://{0}/41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz".format(os.getcwd())
+
+    version('3.0', '7e171b4861b9d514e80aafc3d9cdf554')
+
+    depends_on('perl', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('bowtie', prefix.bowtie)
+        install_tree('bwa', prefix.bwa)
+        install_tree('dotlib', prefix.dotlib)
+        install_tree('tools', prefix.tools)
+        install('SSPACE_Standard_v{0}.pl'.format(self.version), prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('SSPACE_HOME', prefix)
+        run_env.prepend_path('PATH', prefix)