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authorJustin S <3630356+codeandkey@users.noreply.github.com>2020-06-08 01:07:34 -0500
committerGitHub <noreply@github.com>2020-06-08 08:07:34 +0200
commitd9738f569d3eb32d745da4153fbdeeebb14434d9 (patch)
tree5a1ff74c27238b333406dade3a5aca073decfe2f
parentbd1a0a9ad4c9ac19a50c60f75aba6588c8ccfe6c (diff)
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ltr-retriever: new package at v2.8.7 (#16832)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
-rw-r--r--var/spack/repos/builtin/packages/ltr-retriever/package.py45
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)