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| -rw-r--r-- | var/spack/repos/builtin/packages/orthofiller/package.py | 38 |
1 files changed, 38 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/orthofiller/package.py b/var/spack/repos/builtin/packages/orthofiller/package.py new file mode 100644 index 0000000000..1319f721f3 --- /dev/null +++ b/var/spack/repos/builtin/packages/orthofiller/package.py @@ -0,0 +1,38 @@ +# Copyright 2013-2019 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 os + + +class Orthofiller(Package): + """OrthoFiller: Identifying missing annotations for evolutionarily + conserved genes.""" + + homepage = "https://github.com/mpdunne/orthofiller/" + url = "https://github.com/mpdunne/orthofiller/archive/1.1.4.tar.gz" + + version('1.1.4', sha256='a693a3372a3f05041ce30cbf84da1be88e85eae4effe32dbd7809ccef119a295') + + depends_on('augustus', type='run') + depends_on('bedtools2@2.25.0', type='run') + depends_on('hmmer', type='run') + depends_on('orthofinder', type='run') + depends_on('python@2.7:', type='run') + depends_on('py-biopython', type='run') + depends_on('py-scipy', type='run') + depends_on('r', type='run') + depends_on('r-gamlss', type='run') + depends_on('mafft', type='run') + + def install(self, spec, prefix): + # orthofiller tests for common unix programs using man + # runtime modules will quickly overflow the maximum MANPATH; + # we change the man tests to use which instead, more reliable anyway + filter_file('"man "', '"which "', 'OrthoFiller.py', string=True) + + os.chmod('OrthoFiller.py', 0o755) + mkdirp(prefix.bin) + install('OrthoFiller.py', prefix.bin) |