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-rw-r--r--var/spack/repos/builtin/packages/hybpiper/package.py59
-rw-r--r--var/spack/repos/builtin/packages/spades/package.py45
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')