dev-perl/Bio-SamTools: Version bump; remove old

Package-Manager: portage-2.2.26

1 files changed, 50 insertions, 0 deletions

diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
new file mode 100644
index 000000000000..68d73836cb3d
--- /dev/null
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
@@ -0,0 +1,50 @@
+# 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
+}