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| -rw-r--r-- | var/spack/repos/builtin/packages/kaiju/package.py | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/kaiju/package.py b/var/spack/repos/builtin/packages/kaiju/package.py new file mode 100644 index 0000000000..e77e3f529d --- /dev/null +++ b/var/spack/repos/builtin/packages/kaiju/package.py @@ -0,0 +1,48 @@ +############################################################################## +# Copyright (c) 2013-2018, 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 Kaiju(MakefilePackage): + """Kaiju is a program for the taxonomic classification + of high-throughput sequencing reads.""" + + homepage = "https://github.com/bioinformatics-centre/kaiju" + url = "https://github.com/bioinformatics-centre/kaiju/archive/v1.6.2.zip" + + version('1.6.2', '0bd85368954837aa31f3de8b87ea410b') + + build_directory = 'src' + + depends_on('perl-io-compress', type='run') + depends_on('py-htseq', type='run') + + def edit(self, spec, prefix): + # Replace ftp:// with https:// + makedb = FileFilter('util/makeDB.sh') + makedb.filter('ftp://', 'https://', string=True) + + def install(self, spec, prefix): + install_tree('bin', prefix.bin) |