diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/rtax/package.py | 43 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/usearch/package.py | 49 |
2 files changed, 92 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/rtax/package.py b/var/spack/repos/builtin/packages/rtax/package.py new file mode 100644 index 0000000000..c2b917a81e --- /dev/null +++ b/var/spack/repos/builtin/packages/rtax/package.py @@ -0,0 +1,43 @@ +############################################################################## +# 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 Rtax(Package): + """Rapid and accurate taxonomic classification of short paired-end + sequence reads from the 16S ribosomal RNA gene""" + + homepage = "https://github.com/davidsoergel/rtax" + url = "http://static.davidsoergel.com/rtax-0.984.tgz" + + version('0.984', 'e9dbbe4b3c26b0f0f6c14a5fb46aa587') + + depends_on('usearch') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('rtax', prefix.bin) + install_tree('scripts', prefix.bin.scripts) + install_tree('greengenes', prefix.bin.greengenes) diff --git a/var/spack/repos/builtin/packages/usearch/package.py b/var/spack/repos/builtin/packages/usearch/package.py new file mode 100644 index 0000000000..87ea6798ca --- /dev/null +++ b/var/spack/repos/builtin/packages/usearch/package.py @@ -0,0 +1,49 @@ +############################################################################## +# 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 + + +class Usearch(Package): + """USEARCH is a unique sequence analysis tool with thousands of users + world-wide. + + Note: A manual download is required for USEARCH. + Spack will search your current directory for the download file. + Alternatively, add this file to a mirror so that Spack can find it. + For instructions on how to set up a mirror, see + http://spack.readthedocs.io/en/latest/mirrors.html""" + + homepage = "http://www.drive5.com/usearch/" + + version('10.0.240', '05192b6d5e291530c190a19a3cc82b53', expand=False) + + def url_for_version(self, version): + return "file://{0}/usearch{1}_i86linux32".format(os.getcwd(), version) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('usearch{0}_i86linux32'.format(self.version), + prefix.bin.usearch) |