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jlec 14/10/02 10:25:34 |
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Modified: Bio-SamTools-1.390.0-r1.ebuild ChangeLog |
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Log: |
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dev-perl/Bio-SamTools: Make it build with samtools-1, #523568 |
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(Portage version: 2.2.14_rc1/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
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Revision Changes Path |
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1.3 dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild?rev=1.3&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild?rev=1.3&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild?r1=1.2&r2=1.3 |
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Index: Bio-SamTools-1.390.0-r1.ebuild |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild,v |
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retrieving revision 1.2 |
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retrieving revision 1.3 |
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diff -u -r1.2 -r1.3 |
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--- Bio-SamTools-1.390.0-r1.ebuild 24 Sep 2014 07:52:53 -0000 1.2 |
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+++ Bio-SamTools-1.390.0-r1.ebuild 2 Oct 2014 10:25:34 -0000 1.3 |
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@@ -1,12 +1,13 @@ |
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# Copyright 1999-2014 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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-# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild,v 1.2 2014/09/24 07:52:53 jlec Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild,v 1.3 2014/10/02 10:25:34 jlec Exp $ |
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EAPI=5 |
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MODULE_AUTHOR=LDS |
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MODULE_VERSION=1.39 |
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-inherit perl-module |
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+ |
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+inherit perl-module toolchain-funcs |
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DESCRIPTION="Read SAM/BAM database files" |
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@@ -16,8 +17,7 @@ |
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RDEPEND=" |
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sci-biology/bioperl |
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- >=sci-biology/samtools-0.1.16 |
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- <sci-biology/samtools-1 |
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+ >=sci-biology/samtools-1 |
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" |
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DEPEND="${RDEPEND} |
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virtual/perl-ExtUtils-CBuilder |
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@@ -26,7 +26,12 @@ |
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SRC_TEST=do |
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+PATCHES=( |
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+ "${FILESDIR}"/${P}-samtools-1.patch |
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+) |
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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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@@ -34,9 +39,11 @@ |
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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 "bam/khash.h"|' \ |
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- -e 's|#include "faidx.h"|#include "bam/faidx.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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+ |
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+ tc-export CC |
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} |
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1.16 dev-perl/Bio-SamTools/ChangeLog |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog?rev=1.16&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog?rev=1.16&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog?r1=1.15&r2=1.16 |
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Index: ChangeLog |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog,v |
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retrieving revision 1.15 |
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retrieving revision 1.16 |
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diff -u -r1.15 -r1.16 |
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--- ChangeLog 24 Sep 2014 07:52:53 -0000 1.15 |
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+++ ChangeLog 2 Oct 2014 10:25:34 -0000 1.16 |
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@@ -1,6 +1,10 @@ |
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# ChangeLog for dev-perl/Bio-SamTools |
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# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog,v 1.15 2014/09/24 07:52:53 jlec Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog,v 1.16 2014/10/02 10:25:34 jlec Exp $ |
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+ |
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+ 02 Oct 2014; Justin Lecher <jlec@g.o> Bio-SamTools-1.390.0-r1.ebuild, |
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+ +files/Bio-SamTools-1.390.0-samtools-1.patch: |
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+ Make it build with samtools-1, #523568 |
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|
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24 Sep 2014; Justin Lecher <jlec@g.o> -Bio-SamTools-1.330.0.ebuild, |
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-Bio-SamTools-1.370.0-r1.ebuild, -Bio-SamTools-1.380.0.ebuild, |
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