1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
|
# Copyright 2013-2023 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 os import symlink
from spack.package import *
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"
maintainers("snehring")
license("GPL-3.0-only")
version("2.9.4", sha256="a9f4668113d2d75ab97cd85b456f11b00afd4876848a8ef099622ec0d9e505e7")
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")
depends_on("py-tesorter", type="run", when="@2.9.4:")
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.bin, "paths")
filter_file("BLAST=.*", "", "paths")
if spec.satisfies("@2.9.4:"):
filter_file(
"^TEsorter=.*$", "TEsorter={}".format(spec["py-tesorter"].prefix.bin), "paths"
)
mkdirp(prefix.opt)
mkdirp(prefix.bin)
install_tree(".", prefix.opt.ltr_retriever)
symlink(prefix.opt.ltr_retriever.LTR_retriever, prefix.bin.LTR_retriever)
|
