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
|
# Copyright 2013-2018 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 glob import glob
class PerlStarFusion(Package):
"""STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis
Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate
fusion transcripts supported by Illumina reads. STAR-Fusion further
processes the output generated by the STAR aligner to map junction reads
and spanning reads to a reference annotation set."""
homepage = "https://github.com/STAR-Fusion/STAR-Fusion"
git = "https://github.com/STAR-Fusion/STAR-Fusion.git"
version('master', commit='8c5a541')
extends('perl')
depends_on('star', type=('build', 'run'))
depends_on('perl', type=('build', 'run'))
depends_on('perl-intervaltree', type=('build', 'run'))
depends_on('perl-dbi', type=('build', 'run'))
depends_on('perl-dbfile', type=('build', 'run'))
depends_on('perl-uri-escape', type=('build', 'run'))
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('STAR-Fusion', prefix.bin)
mkdirp(perl_lib_dir)
with working_dir('PerlLib'):
for pm in glob("*.pm"):
install(pm, perl_lib_dir)
with working_dir('util'):
for files in glob("*"):
install(files, prefix.bin)
|
