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| author | Justin S <3630356+codeandkey@users.noreply.github.com> | 2020-06-08 01:07:34 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2020-06-08 08:07:34 +0200 |
| commit | d9738f569d3eb32d745da4153fbdeeebb14434d9 (patch) | |
| tree | 5a1ff74c27238b333406dade3a5aca073decfe2f /var | |
| parent | bd1a0a9ad4c9ac19a50c60f75aba6588c8ccfe6c (diff) | |
| download | spack-d9738f569d3eb32d745da4153fbdeeebb14434d9.tar.gz spack-d9738f569d3eb32d745da4153fbdeeebb14434d9.tar.bz2 spack-d9738f569d3eb32d745da4153fbdeeebb14434d9.tar.xz spack-d9738f569d3eb32d745da4153fbdeeebb14434d9.zip | |
ltr-retriever: new package at v2.8.7 (#16832)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/ltr-retriever/package.py | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/ltr-retriever/package.py b/var/spack/repos/builtin/packages/ltr-retriever/package.py new file mode 100644 index 0000000000..2cc7f0a231 --- /dev/null +++ b/var/spack/repos/builtin/packages/ltr-retriever/package.py @@ -0,0 +1,45 @@ +# Copyright 2013-2020 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 * +from os import symlink + + +class LtrRetriever(Package): + """LTR_retriever is a highly accurate and sensitive program for + identification of LTR retrotransposons.""" + + homepage = "https://github.com/oushujun/LTR_retriever" + url = "https://github.com/oushujun/LTR_retriever/archive/v2.8.7.tar.gz" + + version('2.8.7', sha256='29ca6f699c57b5e964aa0ee6c7d3e1e4cd5362dadd789e5f0e8c82fe0bb29369') + + depends_on('perl', type='run') + depends_on('blast-plus', type='run') + depends_on('hmmer@3.1b2:', type='run') + depends_on('cdhit', type='run') + depends_on('repeatmasker', type='run') + + def install(self, spec, prefix): + filter_file(r'BLAST\+=.*', 'BLAST+=%s' % spec['blast-plus'].prefix.bin, + 'paths') + filter_file('RepeatMasker=.*', + 'RepeatMasker=%s' % spec['repeatmasker'].prefix.bin, + 'paths') + filter_file('HMMER=.*', + 'HMMER=%s' % spec['hmmer'].prefix.bin, + 'paths') + filter_file('CDHIT=.*', + 'CDHIT=%s' % spec['cdhit'].prefix, + 'paths') + filter_file('BLAST=.*', '', 'paths') + + mkdirp(prefix.opt) + mkdirp(prefix.bin) + + install_tree('.', prefix.opt.ltr_retriever) + + symlink(prefix.opt.ltr_retriever.LTR_retriever, + prefix.bin.LTR_retriever) |