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Diffstat (limited to 'var/spack/repos/builtin/packages/mirdeep/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/mirdeep/package.py | 67 |
1 files changed, 0 insertions, 67 deletions
diff --git a/var/spack/repos/builtin/packages/mirdeep/package.py b/var/spack/repos/builtin/packages/mirdeep/package.py deleted file mode 100644 index 28981eade5..0000000000 --- a/var/spack/repos/builtin/packages/mirdeep/package.py +++ /dev/null @@ -1,67 +0,0 @@ -############################################################################## -# 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 - - -class Mirdeep(Package): - """miRDeep2 is a completely overhauled tool which discovers microRNA genes - by analyzing sequenced RNAs.""" - - homepage = "https://www.mdc-berlin.de/8551903/en/" - url = "https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep2_0_0_8.zip" - - version('2.0.0.8', 'a707f7d7ad4a2975fb8b2e78c5bcf483') - - depends_on('perl', type=('build', 'run')) - depends_on('perl-pdf-api2', type=('build', 'run')) - depends_on('bowtie') - depends_on('viennarna') - depends_on('squid') - depends_on('randfold') - - def url_for_version(self, version): - url = 'https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep{0}.zip' - return url.format(version.underscored) - - def patch(self): - with working_dir('src'): - files = glob.iglob("*.pl") - for file in files: - change = FileFilter(file) - change.filter('usr/bin/perl', 'usr/bin/env perl') - change.filter('perl -W', 'perl') - change.filter("../Rfam_for_miRDeep.fa", - "Rfam_for_miRDeep.fa") - change.filter("../install_successful", - "install_successful") - - def install(self, spec, prefix): - install_tree('src', prefix.bin) - install('Rfam_for_miRDeep.fa', prefix.bin) - # miRDeep looks for the install_sucessful file to check if you used - # their automated install script which we'll just be kind of hacking - # around - touch(prefix.bin.install_successful) |