bismark: Create new package (#7795)

* bismark: Create new package

* bismark: fix dependency types

1 files changed, 54 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/bismark/package.py b/var/spack/repos/builtin/packages/bismark/package.py
new file mode 100644
index 0000000000..62cb5a0ce9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bismark/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# 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 Bismark(Package):
+    """A tool to map bisulfite converted sequence reads and determine cytosine
+    methylation states"""
+
+    homepage = "https://www.bioinformatics.babraham.ac.uk/projects/bismark"
+    url      = "https://github.com/FelixKrueger/Bismark/archive/0.19.0.tar.gz"
+
+    version('0.19.0', 'f403654aded77bf0d1dac1203867ded1')
+    version('0.18.2', '42334b7e3ed53ba246f30f1f846b4af8')
+
+    depends_on('bowtie2', type='run')
+    depends_on('perl', type='run')
+    depends_on('samtools', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('bam2nuc', prefix.bin)
+        install('bismark', prefix.bin)
+        install('bismark_genome_preparation', prefix.bin)
+        install('bismark_methylation_extractor', prefix.bin)
+        install('bismark2bedGraph', prefix.bin)
+        install('bismark2report', prefix.bin)
+        install('bismark2summary', prefix.bin)
+        install('coverage2cytosine', prefix.bin)
+        install('deduplicate_bismark', prefix.bin)
+        install('filter_non_conversion', prefix.bin)
+        install('NOMe_filtering', prefix.bin)