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| -rw-r--r-- | var/spack/repos/builtin/packages/deconseq-standalone/package.py | 60 |
1 files changed, 60 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/deconseq-standalone/package.py b/var/spack/repos/builtin/packages/deconseq-standalone/package.py new file mode 100644 index 0000000000..ce73ce59a3 --- /dev/null +++ b/var/spack/repos/builtin/packages/deconseq-standalone/package.py @@ -0,0 +1,60 @@ +############################################################################## +# 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 DeconseqStandalone(Package): + """The DeconSeq tool can be used to automatically detect and efficiently + remove sequence contaminations from genomic and metagenomic datasets.""" + + homepage = "http://deconseq.sourceforge.net" + url = "https://sourceforge.net/projects/deconseq/files/standalone/deconseq-standalone-0.4.3.tar.gz" + + version('0.4.3', 'cb3fddb90e584d89fd9c2b6b8f2e20a2') + + depends_on('perl@5:') + + def install(self, spec, prefix): + + filter_file(r'#!/usr/bin/perl', + '#!/usr/bin/env perl', 'deconseq.pl') + filter_file(r'#!/usr/bin/perl', + '#!/usr/bin/env perl', 'splitFasta.pl') + + mkdirp(prefix.bin) + install('bwa64', prefix.bin) + install('bwaMAC', prefix.bin) + install('deconseq.pl', prefix.bin) + install('splitFasta.pl', prefix.bin) + install('DeconSeqConfig.pm', prefix) + + chmod = which('chmod') + chmod('+x', join_path(prefix.bin, 'bwa64')) + chmod('+x', join_path(prefix.bin, 'bwaMAC')) + chmod('+x', join_path(prefix.bin, 'deconseq.pl')) + chmod('+x', join_path(prefix.bin, 'splitFasta.pl')) + + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('PERL5LIB', prefix) |