| # Copyright 1999-2015 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 |
| " |
| 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 |
| } |