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Diffstat (limited to 'var/spack/repos/builtin/packages/mirdeep2/package.py')
-rw-r--r-- | var/spack/repos/builtin/packages/mirdeep2/package.py | 48 |
1 files changed, 48 insertions, 0 deletions
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..cf85705750 --- /dev/null +++ b/var/spack/repos/builtin/packages/mirdeep2/package.py @@ -0,0 +1,48 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +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) |