shortbred: Create new package (#7210)

1 files changed, 51 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/shortbred/package.py b/var/spack/repos/builtin/packages/shortbred/package.py
new file mode 100644
index 0000000000..aeccfa9378
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+++ b/var/spack/repos/builtin/packages/shortbred/package.py
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+##############################################################################
+# Copyright (c) 2013-2017, 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/spack/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 Shortbred(Package):
+    """ShortBRED is a system for profiling protein families of interest at
+    very high specificity in shotgun meta'omic sequencing data."""
+
+    homepage = "https://huttenhower.sph.harvard.edu/shortbred"
+    url      = "https://bitbucket.org/biobakery/shortbred/get/0.9.4.tar.gz"
+
+    version('0.9.4', 'ad3dff344cbea3713e78b384afad28fd')
+
+    depends_on('blast-plus@2.2.28:')
+    depends_on('cdhit@4.6:')
+    depends_on('muscle@3.8.31:')
+    depends_on('python@2.7.9:')
+    depends_on('py-biopython')
+    depends_on('usearch@6.0.307:')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('shortbred_identify.py', prefix.bin)
+        install('shortbred_quantify.py', prefix.bin)
+        install_tree('src', prefix.src)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PYTHONPATH', self.prefix)