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authorAudrey Thoma <las_thoma15@iastate.edu>2017-08-11 13:51:27 -0500
committerAdam J. Stewart <ajstewart426@gmail.com>2017-08-11 13:51:27 -0500
commitd16f823f9d8236eb6261044d2445e1b3dafa402d (patch)
tree5c011590831d5737748a7327c30777b961ad520c
parenta030c858ddeb03ebfe5ec2e4cf115530b07460aa (diff)
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sspace-standard: new pacakge (#5071)
* sspace-standard: new pacakge * fixing install versioning * fixing description
-rw-r--r--var/spack/repos/builtin/packages/sspace-standard/package.py56
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)