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commit: 29bb345f1ea0a356c7e7e4eca3ab3bc405a7d846 |
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Author: Kent Fredric <kentnl <AT> gentoo <DOT> org> |
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AuthorDate: Sun Sep 10 03:20:29 2017 +0000 |
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Commit: Kent Fredric <kentnl <AT> gentoo <DOT> org> |
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CommitDate: Sun Sep 10 03:22:39 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=29bb345f |
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|
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dev-perl/Bio-SamTools: Bump to version 1.430.0 |
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|
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- Links against samtools:0.1-legacy series, as even though this code |
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previously attempted to use 1.0+, closer inspection indicated |
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incomplete linking, missing symbols, and failing tests introduced |
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by this attempt. Additionally, upstream EXPLICITLY STATE the lack of |
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current support for samtools 1.0 |
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|
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- Restores DIST_TEST as I can now test they work |
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|
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- Fold swathe of sed commands into patch |
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|
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Upstream: |
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- Ship some test files requried for tests to pass |
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|
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Closes: https://bugs.gentoo.org/611970 |
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Closes: https://bugs.gentoo.org/604950 |
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Package-Manager: Portage-2.3.6, Repoman-2.3.2 |
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|
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dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild | 33 ++++++++ |
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dev-perl/Bio-SamTools/Manifest | 1 + |
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.../files/Bio-SamTools-1.430.0-legacy.patch | 88 ++++++++++++++++++++++ |
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3 files changed, 122 insertions(+) |
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|
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diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild |
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new file mode 100644 |
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index 00000000000..1147cec5a48 |
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--- /dev/null |
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+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild |
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@@ -0,0 +1,33 @@ |
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+# Copyright 1999-2017 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=6 |
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+ |
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+DIST_AUTHOR=LDS |
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+DIST_VERSION=1.43 |
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+inherit perl-module toolchain-funcs |
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+ |
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+DESCRIPTION="Read SAM/BAM database files" |
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+ |
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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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+ |
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+RDEPEND=" |
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+ >=sci-biology/bioperl-1.6.9 |
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+ sci-biology/samtools:0.1-legacy= |
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+" |
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+DEPEND="${RDEPEND} |
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+ virtual/perl-ExtUtils-CBuilder |
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+ >=dev-perl/Module-Build-0.420.0 |
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+" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}"/${PN}-1.430.0-legacy.patch |
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+) |
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+ |
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+src_prepare() { |
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+ perl-module_src_prepare |
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+ tc-export CC |
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+} |
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|
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diff --git a/dev-perl/Bio-SamTools/Manifest b/dev-perl/Bio-SamTools/Manifest |
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index 733a42f0cc5..f379ea7e384 100644 |
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--- a/dev-perl/Bio-SamTools/Manifest |
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+++ b/dev-perl/Bio-SamTools/Manifest |
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@@ -1 +1,2 @@ |
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DIST Bio-SamTools-1.42.tar.gz 337821 SHA256 ef4b736e86442ce61f56ddd94befc302ccc4646cae3c45407e107400c703584c SHA512 6a1f95104ce91a800a314c304915af9d6e1cc477c7d5f42b640d0a27b18cd32c4ad9e261cac5556f4863652570a3c573d34245963fc4b9ade067981b2a329271 WHIRLPOOL 5a216e51173ee5a9a930013718452bcbfbcffe1aa1663f50d567daf17378a50135b1b0b6d750c9aece05de268e730faf6c54963823c037559fb50ed95dda32c7 |
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+DIST Bio-SamTools-1.43.tar.gz 340833 SHA256 7085ee5e97ad75dbbebd8583072d67b2b06d29e7a9f9741c9ac58dabe300d3fd SHA512 cd5bc6213c093f5105399c95278803afcc537bb3d191686cda0193b82fda2580749bf7533791899939a78963fcc0d6b36eabe9c309c9c6816a9849e3c892c41b WHIRLPOOL cd5ece1f08e2b4c8c64c4d289abc7a7035c18f725c28df4e9ac0319efdabb2137864b6d0b692928469c4c48010bf0ab823990a2074cef4c1a87707f5fd3f31e4 |
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|
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diff --git a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch |
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new file mode 100644 |
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index 00000000000..8464f06a2f0 |
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--- /dev/null |
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+++ b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch |
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@@ -0,0 +1,88 @@ |
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+From 74b38ded97f7a1940c3a37b9aec9b3287a3a78bd Mon Sep 17 00:00:00 2001 |
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+From: Kent Fredric <kentfredric@×××××.com> |
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+Date: Sun, 10 Sep 2017 13:33:32 +1200 |
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+Subject: Fix linking/compiling for bam-0.1-legacy |
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+ |
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+--- |
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+ Build.PL | 6 +++--- |
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+ c_bin/bam2bedgraph.c | 2 +- |
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+ c_bin/makefile | 6 +++--- |
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+ lib/Bio/DB/Sam.xs | 6 +++--- |
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+ 4 files changed, 10 insertions(+), 10 deletions(-) |
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+ |
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+diff --git a/Build.PL b/Build.PL |
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+index 685815f..2611759 100644 |
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+--- a/Build.PL |
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++++ b/Build.PL |
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+@@ -4,8 +4,8 @@ use strict; |
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+ use Module::Build; |
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+ use Module::Load::Conditional qw(can_load); |
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+ |
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+-my $HeaderFile = "bam.h"; |
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+-my $LibFile = "libbam.a"; |
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++my $HeaderFile = "bam-0.1-legacy/bam.h"; |
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++my $LibFile = "libbam-0.1-legacy.so"; |
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+ my $ReadLine; |
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+ |
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+ my ($sam_include,$sam_lib) = find_sam(); # may exit with error here |
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+@@ -39,7 +39,7 @@ my $build = $class->new( |
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+ dist_abstract => 'Perl interface to SamTools library for DNA sequencing', |
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+ license => 'perl', |
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+ include_dirs => [$sam_include], |
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+- extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'], |
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++ extra_linker_flags => ["-L$sam_lib",'-lbam-0.1-legacy','-lpthread','-lz'], |
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+ |
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+ extra_compiler_flags=>[ |
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+ |
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+diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c |
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+index 298e9a8..91218fa 100644 |
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+--- a/c_bin/bam2bedgraph.c |
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++++ b/c_bin/bam2bedgraph.c |
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+@@ -1,5 +1,5 @@ |
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+ #include <stdio.h> |
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+-#include "sam.h" |
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++#include "bam-0.1-legacy/sam.h" |
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+ |
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+ typedef struct { |
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+ uint32_t ltid; |
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+diff --git a/c_bin/makefile b/c_bin/makefile |
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+index 9aef917..0abbb4c 100644 |
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+--- a/c_bin/makefile |
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++++ b/c_bin/makefile |
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+@@ -1,5 +1,5 @@ |
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+-CC= gcc |
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+-CFLAGS= -g -Wall -O2 -fPIC |
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++CC?= gcc |
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++CFLAGS?= -g -Wall -O2 -fPIC |
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+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 |
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+ INCLUDES= |
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+ LIBPATH= |
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+@@ -14,7 +14,7 @@ PROG= bam2bedgraph |
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+ all:$(PROG) |
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+ |
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+ bam2bedgraph: bam2bedgraph.o |
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+- $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lpthread -lm -lz |
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++ $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam-0.1-legacy -lpthread -lm -lz |
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+ |
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+ clean: |
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+ rm -f *.o $(PROG) |
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+diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs |
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+index 023f655..86410fb 100644 |
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+--- a/lib/Bio/DB/Sam.xs |
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++++ b/lib/Bio/DB/Sam.xs |
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+@@ -25,9 +25,9 @@ |
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+ |
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+ #include <unistd.h> |
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+ #include <math.h> |
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+-#include "bam.h" |
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+-#include "khash.h" |
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+-#include "faidx.h" |
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++#include "bam-0.1-legacy/bam.h" |
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++#include "bam-0.1-legacy/khash.h" |
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++#include "bam-0.1-legacy/faidx.h" |
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+ |
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+ /* stolen from bam_aux.c */ |
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+ #define MAX_REGION 1<<29 |
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+-- |
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+2.14.1 |
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+ |