diff options
Diffstat (limited to 'dev-perl/Bio-SamTools')
-rw-r--r-- | dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild | 33 | ||||
-rw-r--r-- | dev-perl/Bio-SamTools/Manifest | 4 | ||||
-rw-r--r-- | dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch | 88 | ||||
-rw-r--r-- | dev-perl/Bio-SamTools/metadata.xml | 32 |
4 files changed, 157 insertions, 0 deletions
diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild new file mode 100644 index 000000000000..1147cec5a486 --- /dev/null +++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DIST_AUTHOR=LDS +DIST_VERSION=1.43 +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:0.1-legacy= +" +DEPEND="${RDEPEND} + virtual/perl-ExtUtils-CBuilder + >=dev-perl/Module-Build-0.420.0 +" + +PATCHES=( + "${FILESDIR}"/${PN}-1.430.0-legacy.patch +) + +src_prepare() { + perl-module_src_prepare + tc-export CC +} diff --git a/dev-perl/Bio-SamTools/Manifest b/dev-perl/Bio-SamTools/Manifest new file mode 100644 index 000000000000..9130d1cf0d4e --- /dev/null +++ b/dev-perl/Bio-SamTools/Manifest @@ -0,0 +1,4 @@ +AUX Bio-SamTools-1.430.0-legacy.patch 2466 BLAKE2B ab4a384031f4f2b333700e9ddf62d7a8293f88c0390b8f151a6b0657f4f59613f1e33d259f9b575fb8348593dfdc408e4d6168ecba3c3863a856f3ef6abefa9f SHA512 3e886216a966144aa69aa86d3ffa28ee8f9aadec84f760259aad9fcdc09ca69499655e8c3d81a5b39d79fd503f14e0159bdf2422d66458f1e9095b2fb05da26a +DIST Bio-SamTools-1.43.tar.gz 340833 BLAKE2B 2b488667b86ef1bedb7cf74dfdcb3abc0302d9f309c1fc3077682bb400c8307f3b7d8fb1a9015a26f9a17f9e9955845d160512aa3273c368b720fe51b4392458 SHA512 cd5bc6213c093f5105399c95278803afcc537bb3d191686cda0193b82fda2580749bf7533791899939a78963fcc0d6b36eabe9c309c9c6816a9849e3c892c41b +EBUILD Bio-SamTools-1.430.0.ebuild 591 BLAKE2B d92daf9d86f1d8a4b60257fd810d012794d41e7082555a89b1fa66f2f2bb65b2585a27d68684d2dd1820dda214905868c752bbcbf3083e32d1797848cfaae4cc SHA512 fe282e0404be9a758e1f42ec9d12ae1dd935aa0f9fca8d07e07f55ae6453b2c615868de859b4e5af9f2195c18b988f0ac8132db0c8c0a880843178bce041b221 +MISC metadata.xml 1642 BLAKE2B 8e00b2305f870d0007a22f366376d77d359df2ab54d279da2c7b791da320f72e7d110956251c3adcddaf8b4b318110b5ff4b6cde4a6cd359cbb403f666c7de93 SHA512 d518abd6c3f99c370ce401f7fce792b2d55d29fc2baccb54f8a32f2e2c385acf3dd7f31f3c3fc0764fb3b754e4bd3378eef0002a0e4d48b2ae2a116c85379c50 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 new file mode 100644 index 000000000000..8464f06a2f01 --- /dev/null +++ b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.430.0-legacy.patch @@ -0,0 +1,88 @@ +From 74b38ded97f7a1940c3a37b9aec9b3287a3a78bd Mon Sep 17 00:00:00 2001 +From: Kent Fredric <kentfredric@gmail.com> +Date: Sun, 10 Sep 2017 13:33:32 +1200 +Subject: Fix linking/compiling for bam-0.1-legacy + +--- + Build.PL | 6 +++--- + c_bin/bam2bedgraph.c | 2 +- + c_bin/makefile | 6 +++--- + lib/Bio/DB/Sam.xs | 6 +++--- + 4 files changed, 10 insertions(+), 10 deletions(-) + +diff --git a/Build.PL b/Build.PL +index 685815f..2611759 100644 +--- a/Build.PL ++++ b/Build.PL +@@ -4,8 +4,8 @@ use strict; + use Module::Build; + use Module::Load::Conditional qw(can_load); + +-my $HeaderFile = "bam.h"; +-my $LibFile = "libbam.a"; ++my $HeaderFile = "bam-0.1-legacy/bam.h"; ++my $LibFile = "libbam-0.1-legacy.so"; + my $ReadLine; + + my ($sam_include,$sam_lib) = find_sam(); # may exit with error here +@@ -39,7 +39,7 @@ my $build = $class->new( + dist_abstract => 'Perl interface to SamTools library for DNA sequencing', + license => 'perl', + include_dirs => [$sam_include], +- extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'], ++ extra_linker_flags => ["-L$sam_lib",'-lbam-0.1-legacy','-lpthread','-lz'], + + extra_compiler_flags=>[ + +diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c +index 298e9a8..91218fa 100644 +--- a/c_bin/bam2bedgraph.c ++++ b/c_bin/bam2bedgraph.c +@@ -1,5 +1,5 @@ + #include <stdio.h> +-#include "sam.h" ++#include "bam-0.1-legacy/sam.h" + + typedef struct { + uint32_t ltid; +diff --git a/c_bin/makefile b/c_bin/makefile +index 9aef917..0abbb4c 100644 +--- a/c_bin/makefile ++++ b/c_bin/makefile +@@ -1,5 +1,5 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 -fPIC ++CC?= gcc ++CFLAGS?= -g -Wall -O2 -fPIC + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 + INCLUDES= + LIBPATH= +@@ -14,7 +14,7 @@ PROG= bam2bedgraph + all:$(PROG) + + bam2bedgraph: bam2bedgraph.o +- $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lpthread -lm -lz ++ $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam-0.1-legacy -lpthread -lm -lz + + clean: + rm -f *.o $(PROG) +diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs +index 023f655..86410fb 100644 +--- a/lib/Bio/DB/Sam.xs ++++ b/lib/Bio/DB/Sam.xs +@@ -25,9 +25,9 @@ + + #include <unistd.h> + #include <math.h> +-#include "bam.h" +-#include "khash.h" +-#include "faidx.h" ++#include "bam-0.1-legacy/bam.h" ++#include "bam-0.1-legacy/khash.h" ++#include "bam-0.1-legacy/faidx.h" + + /* stolen from bam_aux.c */ + #define MAX_REGION 1<<29 +-- +2.14.1 + diff --git a/dev-perl/Bio-SamTools/metadata.xml b/dev-perl/Bio-SamTools/metadata.xml new file mode 100644 index 000000000000..268cc35b8f8c --- /dev/null +++ b/dev-perl/Bio-SamTools/metadata.xml @@ -0,0 +1,32 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="project"> + <email>perl@gentoo.org</email> + <name>Gentoo Perl Project</name> + </maintainer> + <upstream> + <remote-id type="cpan">Bio-SamTools</remote-id> + <remote-id type="cpan-module">Bio::DB::Bam</remote-id> + <remote-id type="cpan-module">Bio::DB::Bam::AlignWrapper</remote-id> + <remote-id type="cpan-module">Bio::DB::Bam::Alignment</remote-id> + <remote-id type="cpan-module">Bio::DB::Bam::FetchIterator</remote-id> + <remote-id type="cpan-module">Bio::DB::Bam::Pileup</remote-id> + <remote-id type="cpan-module">Bio::DB::Bam::PileupWrapper</remote-id> + <remote-id type="cpan-module">Bio::DB::Bam::Query</remote-id> + <remote-id type="cpan-module">Bio::DB::Bam::ReadIterator</remote-id> + <remote-id type="cpan-module">Bio::DB::Bam::SplitAlignmentPart</remote-id> + <remote-id type="cpan-module">Bio::DB::Bam::Target</remote-id> + <remote-id type="cpan-module">Bio::DB::Sam</remote-id> + <remote-id type="cpan-module">Bio::DB::Sam::Constants</remote-id> + <remote-id type="cpan-module">Bio::DB::Sam::Fai</remote-id> + <remote-id type="cpan-module">Bio::DB::Sam::SamToGBrowse</remote-id> + <remote-id type="cpan-module">Bio::DB::Sam::Segment</remote-id> + <remote-id type="cpan-module">Bio::DB::Sam::Segment::Iterator</remote-id> + <remote-id type="cpan-module">Bio::SeqFeature::Coverage</remote-id> + </upstream> +</pkgmetadata> |