Create new package: fastgbs and its dependency platypus. (#8174)

* pushing partially done recipe for fast-gbs and platypus

* modify platypus

* change header

* fast-gbs: change dependency type.

* modify dependency type.

* modify dependency type.

* fast-gbs: Change dependency type to run.

2 files changed, 97 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/fast-gbs/package.py b/var/spack/repos/builtin/packages/fast-gbs/package.py
new file mode 100644
index 0000000000..0805539630
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fast-gbs/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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 FastGbs(Package):
+    """A bioinformatic pipeline designed to extract a high-quality SNP catalog
+       starting from FASTQ files obtained from sequencing
+       genotyping-by-sequencing (GBS) libraries."""
+
+    homepage = "https://bitbucket.org/jerlar73/fast-gbs"
+    url      = "https://bitbucket.org/jerlar73/fast-gbs"
+
+    version('2017-01-25', git='https://bitbucket.org/jerlar73/fast-gbs.git', commit='3b3cbffa84d269419692067c6a3de08b3b88849c')
+
+    depends_on('parallel', type='run')
+    depends_on('python@2.7:', type='run')
+    depends_on('sabre', type='run')
+    depends_on('py-cutadapt', type='run')
+    depends_on('bwa', type='run')
+    depends_on('samtools', type='run')
+    depends_on('platypus', type='run')
+    depends_on('py-pyvcf', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('fastgbs.sh', prefix.bin)
+        install('parameters.txt', prefix.bin)
+        install('makeDir.sh', prefix.bin)
+        install('makeBarcodeSabre.py', prefix.bin)
+        install('vcf2txt.py', prefix.bin)
+        install('txt2unix.sh', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/platypus/package.py b/var/spack/repos/builtin/packages/platypus/package.py
new file mode 100644
index 0000000000..26a20d9576
--- /dev/null
+++ b/var/spack/repos/builtin/packages/platypus/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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 Platypus(Package):
+    """A Haplotype-Based Variant Caller For Next Generation Sequence Data"""
+
+    homepage = "http://www.well.ox.ac.uk/platypus"
+    url      = "http://www.well.ox.ac.uk/bioinformatics/Software/Platypus-latest.tgz"
+
+    version('0.8.1', 'edf3fb5bf080241ddb75a413c8529d57')
+
+    depends_on('python@2.6:', type=('build', 'run'))
+    depends_on('py-cython', type='build')
+    depends_on('htslib')
+
+    def install(self, spec, prefix):
+        buildPlatypus = Executable('./buildPlatypus.sh')
+        buildPlatypus()
+        install_tree('.', prefix.bin)