bsseeker2: new package (#4770)

1 files changed, 49 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/bsseeker2/package.py b/var/spack/repos/builtin/packages/bsseeker2/package.py
new file mode 100644
index 0000000000..aca1e70b01
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bsseeker2/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# 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 Bsseeker2(Package):
+    """A versatile aligning pipeline for bisulfite sequencing data."""
+
+    homepage = "http://pellegrini.mcdb.ucla.edu/BS_Seeker2"
+    url      = "https://github.com/BSSeeker/BSseeker2/archive/v2.1.2.tar.gz"
+
+    version('2.1.2',     '5f7f0ef4071711e56b59c5c16b7f34a7')
+
+    depends_on('python@2.6:2.999', type=('build', 'run'))
+    depends_on('py-pysam', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('Antisense.py', prefix.bin)
+        install_tree('bs_index', prefix.bin.bs_index)
+        install('bs_seeker2-build.py', prefix.bin)
+        install_tree('bs_utils', prefix.bin.bs_utils)
+        install_tree('galaxy', prefix.bin.galaxy)
+        install_tree('bs_align', prefix.bin.bs_align)
+        install('bs_seeker2-align.py', prefix.bin)
+        install('bs_seeker2-call_methylation.py', prefix.bin)
+        install('FilterReads.py', prefix.bin)