50 lines
1.1 KiB
Bash
50 lines
1.1 KiB
Bash
# Copyright 1999-2015 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Id$
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EAPI=6
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DIST_AUTHOR=LDS
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DIST_VERSION=1.42
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inherit perl-module toolchain-funcs
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DESCRIPTION="Read SAM/BAM database files"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE=""
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LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
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RDEPEND="
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>=sci-biology/bioperl-1.6.9
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>=sci-biology/samtools-1
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"
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DEPEND="${RDEPEND}
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virtual/perl-ExtUtils-CBuilder
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>=dev-perl/Module-Build-0.420.0
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"
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DIST_TEST=skip
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# cannot load its own library, fundamentally b0rken
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PATCHES=(
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"${FILESDIR}"/${PN}-1.390.0-samtools-1.patch
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)
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src_prepare() {
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find . -type f -exec chmod +w '{}' + || die
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sed \
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-e 's|my $HeaderFile = "bam.h";|my $HeaderFile = "bam/bam.h";|' \
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-e 's|my $LibFile = "libbam.a";|my $LibFile = "libbam.so";|' \
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-i Build.PL || die
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sed \
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-e 's|#include "bam.h"|#include "bam/bam.h"|' \
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-e 's|#include "sam.h"|#include "bam/sam.h"|' \
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-e 's|#include "khash.h"|#include "htslib/khash.h"|' \
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-e 's|#include "faidx.h"|#include "htslib/faidx.h"|' \
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-i lib/Bio/DB/Sam.xs c_bin/bam2bedgraph.c || die
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perl-module_src_prepare
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tc-export CC
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}
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