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
51
52
53
54
|
# Copyright 2013-2022 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)
import os
from spack.package import *
class EaUtils(MakefilePackage):
"""Command-line tools for processing biological sequencing data. Barcode
demultiplexing, adapter trimming, etc. Primarily written to support an
Illumina based pipeline - but should work with any FASTQs."""
homepage = "https://expressionanalysis.github.io/ea-utils/"
url = "https://github.com/ExpressionAnalysis/ea-utils/archive/1.04.807.tar.gz"
git = "https://github.com/ExpressionAnalysis/ea-utils.git"
maintainers = ['snehring']
version('2021-10-20', commit='10c21926a4dce4289d5052acfd73b8e744d4fede')
version('1.04.807', sha256='aa09d25e6aa7ae71d2ce4198a98e58d563f151f8ff248e4602fa437f12b8d05f',
deprecated=True)
depends_on('sparsehash')
depends_on('zlib')
depends_on('gsl')
depends_on('bamtools')
depends_on('perl', type=['build', 'run'])
build_directory = 'clipper'
def edit(self, spec, prefix):
with working_dir(self.build_directory):
filter_file('/usr', prefix, 'Makefile')
# remove tests from all rule
filter_file(r'^all:.*$', 'all: $(BIN)', 'Makefile')
# remove the vendored sparsehash
filter_file(' sparsehash', '', 'Makefile')
# replace system perl references
for f in next(os.walk(os.getcwd()))[2]:
filter_file('/usr/bin/perl', spec['perl'].prefix.bin.perl, f)
# fix up test script require path
tests = ['join.t', 'mcf.t', 'multx.t']
rep = 'require "{0}";'.format(os.path.join(os.getcwd(),
't', 'test-prep.pl'))
for f in tests:
filter_file(r'^require.*$', rep, os.path.join(os.getcwd(),
't', f))
def flag_handler(self, name, flags):
if name.lower() == 'cxxflags':
flags.append(self.compiler.cxx11_flag)
return (flags, None, None)
|
