From 2bf140601b3f5ccbe2c0a70ed6740209971392c5 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Mon, 17 Jul 2017 12:02:17 -0500 Subject: bsseeker2: new package (#4770) --- .../repos/builtin/packages/bsseeker2/package.py | 49 ++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 var/spack/repos/builtin/packages/bsseeker2/package.py 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) -- cgit v1.2.3-70-g09d2