From bc73e85af8fe4d3e4fef13fa3a1d7031a5cd9cd4 Mon Sep 17 00:00:00 2001 From: Sinan Date: Wed, 23 May 2018 05:25:42 -0700 Subject: Package/mirdeep/fix for new url take2 (#8247) * rename: mirdeep -> mirdeep2 * fixes for new url --- .../repos/builtin/packages/mirdeep/package.py | 67 ---------------------- .../repos/builtin/packages/mirdeep2/package.py | 67 ++++++++++++++++++++++ 2 files changed, 67 insertions(+), 67 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/mirdeep/package.py create mode 100644 var/spack/repos/builtin/packages/mirdeep2/package.py 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 60f5aaaac9..0000000000 --- a/var/spack/repos/builtin/packages/mirdeep/package.py +++ /dev/null @@ -1,67 +0,0 @@ -############################################################################## -# 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 * -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) diff --git a/var/spack/repos/builtin/packages/mirdeep2/package.py b/var/spack/repos/builtin/packages/mirdeep2/package.py new file mode 100644 index 0000000000..02218c4da4 --- /dev/null +++ b/var/spack/repos/builtin/packages/mirdeep2/package.py @@ -0,0 +1,67 @@ +############################################################################## +# 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 * +import glob + + +class Mirdeep2(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/system/files/migrated_files/fiona/mirdeep2_0_0_8.zip" + + version('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/system/files/migrated_files/fiona/mirdeep2_{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) -- cgit v1.2.3-60-g2f50