diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/hybpiper/package.py | 59 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/spades/package.py | 45 |
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') |