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
|
# 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 spack.package import *
class PrinseqLite(Package):
"""PRINSEQ will help you to preprocess your genomic or metagenomic
sequence data in FASTA or FASTQ format."""
homepage = "http://prinseq.sourceforge.net"
url = "https://sourceforge.net/projects/prinseq/files/standalone/prinseq-lite-0.20.4.tar.gz"
version("0.20.4", sha256="9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f")
variant("nopca", default=True, description="Graphs version without PCA")
depends_on("perl", type="run")
depends_on("perl-cairo", type="run")
depends_on("perl-digest-md5", type="run")
depends_on("perl-json", type="run")
def install(self, spec, prefix):
mkdirp(prefix.bin)
filter_file(r"#!/usr/bin/perl", "#!/usr/bin/env perl", "prinseq-graphs-noPCA.pl")
filter_file(r"#!/usr/bin/perl", "#!/usr/bin/env perl", "prinseq-lite.pl")
install("prinseq-graphs-noPCA.pl", prefix.bin)
install("prinseq-lite.pl", prefix.bin)
chmod = which("chmod")
chmod("+x", join_path(self.prefix.bin, "prinseq-graphs-noPCA.pl"))
chmod("+x", join_path(self.prefix.bin, "prinseq-lite.pl"))
|
