diff options
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/jellyfish/package.py | 38 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/kraken/package.py | 51 |
2 files changed, 89 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/jellyfish/package.py b/var/spack/repos/builtin/packages/jellyfish/package.py new file mode 100644 index 0000000000..e6d65838a1 --- /dev/null +++ b/var/spack/repos/builtin/packages/jellyfish/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2017, 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/spack/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 Jellyfish(AutotoolsPackage): + """JELLYFISH is a tool for fast, memory-efficient counting of k-mers in + DNA.""" + + homepage = "http://www.cbcb.umd.edu/software/jellyfish/" + url = "http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz" + + version('1.1.11', 'dc994ea8b0896156500ea8c648f24846') + + depends_on('perl', type=('build', 'run')) + depends_on('python', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/kraken/package.py b/var/spack/repos/builtin/packages/kraken/package.py new file mode 100644 index 0000000000..3994c8c138 --- /dev/null +++ b/var/spack/repos/builtin/packages/kraken/package.py @@ -0,0 +1,51 @@ +############################################################################## +# Copyright (c) 2013-2017, 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/spack/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 Kraken(Package): + """Kraken is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies.""" + + homepage = "https://ccb.jhu.edu/software/kraken/" + url = "https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz" + + version('1.0', 'e790d6b09662bbd810aa34517ef66586') + + depends_on('perl', type=('build', 'run')) + # Does NOT support JELLYFISH 2.0. Ver 1.1.11 is the last version of + # JELLYFISH 1. + depends_on('jellyfish@1.1.11', when='@1.0') + + def install(self, spec, prefix): + installer = Executable('./install_kraken.sh') + installer(self.stage.source_path) + mkdirp(prefix.bin) + files = glob.iglob('*') + for file in files: + if os.path.isfile(file): + install(file, prefix.bin) |