Version bump

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key 0B08240A96F66571)

2 files changed, 58 insertions, 2 deletions

diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild
new file mode 100644
index 000000000000..24d0eaee9b5e
--- /dev/null
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.410.0.ebuild,v 1.1 2015/04/18 18:48:04 dilfridge Exp $
+
+EAPI=5
+
+MODULE_AUTHOR=LDS
+MODULE_VERSION=1.41
+
+inherit perl-module toolchain-funcs
+
+DESCRIPTION="Read SAM/BAM database files"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	>=sci-biology/bioperl-1.6.9
+	>=sci-biology/samtools-1
+"
+DEPEND="${RDEPEND}
+	virtual/perl-ExtUtils-CBuilder
+	>=virtual/perl-Module-Build-0.420.0
+"
+
+SRC_TEST=skip
+# cannot load its own library, fundamentally b0rken
+
+PATCHES=(
+	"${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
+}
diff --git a/dev-perl/Bio-SamTools/ChangeLog b/dev-perl/Bio-SamTools/ChangeLog
index 2363a22a8a2d..05eb774d48bc 100644
--- a/dev-perl/Bio-SamTools/ChangeLog
+++ b/dev-perl/Bio-SamTools/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for dev-perl/Bio-SamTools
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog,v 1.17 2015/04/07 14:12:32 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog,v 1.18 2015/04/18 18:48:04 dilfridge Exp $
+
+*Bio-SamTools-1.410.0 (18 Apr 2015)
+
+  18 Apr 2015; Andreas K. Huettel <dilfridge@gentoo.org>
+  +Bio-SamTools-1.410.0.ebuild:
+  Version bump
 
   02 Oct 2014; Justin Lecher <jlec@gentoo.org> Bio-SamTools-1.390.0-r1.ebuild,
   +files/Bio-SamTools-1.390.0-samtools-1.patch: