blob: 544343818332b4f2d385a7ac894493ce58660b25 (
plain)
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 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=6
DIST_AUTHOR=LDS
DIST_VERSION=1.42
inherit perl-module toolchain-funcs
DESCRIPTION="Read SAM/BAM database files"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
RDEPEND="
>=sci-biology/bioperl-1.6.9
>=sci-biology/samtools-1:0
"
DEPEND="${RDEPEND}
virtual/perl-ExtUtils-CBuilder
>=dev-perl/Module-Build-0.420.0
"
DIST_TEST=skip
# cannot load its own library, fundamentally b0rken
PATCHES=(
"${FILESDIR}"/${PN}-1.390.0-samtools-1.patch
)
src_prepare() {
find . -type f -exec chmod +w '{}' + || die
sed \
-e 's|my $HeaderFile = "bam.h";|my $HeaderFile = "bam/bam.h";|' \
-e 's|my $LibFile = "libbam.a";|my $LibFile = "libbam.so";|' \
-i Build.PL || die
sed \
-e 's|#include "bam.h"|#include "bam/bam.h"|' \
-e 's|#include "sam.h"|#include "bam/sam.h"|' \
-e 's|#include "khash.h"|#include "htslib/khash.h"|' \
-e 's|#include "faidx.h"|#include "htslib/faidx.h"|' \
-i lib/Bio/DB/Sam.xs c_bin/bam2bedgraph.c || die
perl-module_src_prepare
tc-export CC
}
|
GitWeb
