hybpiper: new package (#4720)

* hybpiper: new package and spades dependency

* hybpiper: making flkae8 happy

* hybpiper: fixing dependency errors

* fixing python dep type

* removing cmake from spade dependencies

2 files changed, 104 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/hybpiper/package.py b/var/spack/repos/builtin/packages/hybpiper/package.py
new file mode 100644
index 0000000000..a9e49cef90
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hybpiper/package.py
@@ -0,0 +1,59 @@
+##############################################################################
+# 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 *
+import glob
+import os
+
+
+class Hybpiper(Package):
+    """HybPiper was designed for targeted sequence capture, in which DNA
+       sequencing libraries are enriched for gene regions of interest,
+       especially for phylogenetics. HybPiper is a suite of Python scripts
+       that wrap and connect bioinformatics tools in order to extract target
+       sequences from high-throughput DNA sequencing reads"""
+
+    homepage = "https://github.com/mossmatters/HybPiper"
+    url      = "https://github.com/mossmatters/HybPiper/archive/v1.2.0.tar.gz"
+
+    version('1.2.0', '0ad78e9ca5e3f23ae0eb6236b07e1780')
+
+    depends_on('python@2.7:', type=('build', 'run'))
+    depends_on('py-biopython', type=('build', 'run'))
+    depends_on('exonerate')
+    depends_on('blast-plus')
+    depends_on('spades')
+    depends_on('parallel')
+    depends_on('bwa')
+    depends_on('samtools')
+
+    def setup_envionment(self, spack_env, run_env):
+        run_env.set('HYBPIPER_HOME', prefix)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        files = glob.iglob("*.py")
+        for file in files:
+            if os.path.isfile(file):
+                install(file, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/spades/package.py b/var/spack/repos/builtin/packages/spades/package.py
new file mode 100644
index 0000000000..c7e4469f5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spades/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# 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 Spades(CMakePackage):
+    """SPAdes - St. Petersburg genome assembler - is intended for both
+       standard isolates and single-cell MDA bacteria assemblies."""
+
+    homepage = "http://cab.spbu.ru/software/spades/"
+    url      = "http://cab.spbu.ru/files/release3.10.1/SPAdes-3.10.1.tar.gz"
+
+    version('3.10.1', 'dcab7d145af81b59cc867562f27536c3')
+
+    depends_on('python', type=('build', 'run'))
+    depends_on('zlib')
+    depends_on('bzip2')
+
+    conflicts('%gcc@7.1.0:')
+
+    @property
+    def root_cmakelists_dir(self):
+        return join_path(self.stage.source_path, 'src')