diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/augustus/package.py | 1 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/braker/package.py | 52 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/genemark-et/package.py | 53 |
3 files changed, 106 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index ccaa2f1e70..8a90de639e 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -32,6 +32,7 @@ class Augustus(MakefilePackage): homepage = "http://bioinf.uni-greifswald.de/augustus/" url = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz" + version('3.3', '9ebe494df78ebf6a43091cfc8551050c') version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830') depends_on('bamtools') diff --git a/var/spack/repos/builtin/packages/braker/package.py b/var/spack/repos/builtin/packages/braker/package.py new file mode 100644 index 0000000000..cfc1f16025 --- /dev/null +++ b/var/spack/repos/builtin/packages/braker/package.py @@ -0,0 +1,52 @@ +############################################################################## +# 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 Braker(Package): + """BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation + that combines the advantages of GeneMark-ET and AUGUSTUS""" + + homepage = "http://exon.gatech.edu/braker1.html" + url = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1_v1.11.tar.gz" + + version('1.11', '297efe4cabdd239b710ac2c45d81f6a5') + + depends_on('perl', type=('build', 'run')) + depends_on('augustus') + depends_on('genemark-et') + depends_on('bamtools') + depends_on('samtools') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + mkdirp(prefix.lib) + install('braker.pl', prefix.bin) + install('filterGenemark.pl', prefix.bin) + install('filterIntronsFindStrand.pl', prefix.bin) + install('helpMod.pm', prefix.lib) + + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('PERL5LIB', prefix.lib) diff --git a/var/spack/repos/builtin/packages/genemark-et/package.py b/var/spack/repos/builtin/packages/genemark-et/package.py new file mode 100644 index 0000000000..352f728290 --- /dev/null +++ b/var/spack/repos/builtin/packages/genemark-et/package.py @@ -0,0 +1,53 @@ +############################################################################## +# 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 os +import glob + + +class GenemarkEt(Package): + """Gene Prediction in Bacteria, archaea, Metagenomes and + Metatranscriptomes.""" + + homepage = "http://topaz.gatech.edu/GeneMark" + + version('4.33', '4ab7d7d3277a685dfb49e11bc5b493c3') + + depends_on('perl', type=('build', 'run')) + + def url_for_version(self, version): + return "file://{0}/gm_et_linux_64.tar.gz".format(os.getcwd()) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + with working_dir('gmes_petap'): + install_tree('lib', prefix.lib) + files = glob.iglob('*') + for file in files: + if os.path.isfile(file): + install(file, prefix.bin) + + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('PERL5LIB', prefix.lib) |