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| author |   Marek Szuba <marecki@gentoo.org> | 2018-04-26 12:25:15 +0100 |
|---|---|---|
| committer | Marek Szuba <marecki@gentoo.org> | 2018-04-26 12:30:28 +0100 |
| commit | 9a9cafec65f1eb3de700a077dae30537993823cc (patch) | |
| tree | 3e4212fd6c27372203cb3b09eccdacd052db9863 /dev-perl | |
| parent | sys-apps/restorecond: bump to 2.8_rc1 (diff) | |
| download | gentoo-9a9cafec65f1eb3de700a077dae30537993823cc.tar.gz gentoo-9a9cafec65f1eb3de700a077dae30537993823cc.tar.bz2 gentoo-9a9cafec65f1eb3de700a077dae30537993823cc.zip | |
dev-perl/Bio-DB-HTS: new package
Perl bindings for sci-libs/htslib, used by e.g. Ensembl.
Package-Manager: Portage-2.3.24, Repoman-2.3.6
Diffstat (limited to 'dev-perl')
| -rw-r--r-- | dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild | 30 | ||||
| -rw-r--r-- | dev-perl/Bio-DB-HTS/Manifest | 1 | ||||
| -rw-r--r-- | dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch | 29 | ||||
| -rw-r--r-- | dev-perl/Bio-DB-HTS/metadata.xml | 17 |
4 files changed, 77 insertions, 0 deletions
diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild new file mode 100644 index 000000000000..02c38cd34f33 --- /dev/null +++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DIST_AUTHOR=AVULLO +DIST_VERSION=2.10 + +inherit perl-module + +DESCRIPTION="Perl bindings for sci-libs/htslib" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND="sci-libs/htslib:=" +DEPEND="${RDEPEND} + dev-perl/Module-Build + test? ( dev-perl/Test-LeakTrace )" + +PATCHES=( + "${FILESDIR}/2.10-build_search_for_so.patch" +) + +src_configure() { + local myconf="--htslib=${EPREFIX}/usr" + perl-module_src_configure +} diff --git a/dev-perl/Bio-DB-HTS/Manifest b/dev-perl/Bio-DB-HTS/Manifest new file mode 100644 index 000000000000..536315137fa5 --- /dev/null +++ b/dev-perl/Bio-DB-HTS/Manifest @@ -0,0 +1 @@ +DIST Bio-DB-HTS-2.10.tar.gz 5245650 BLAKE2B a52d9b1e19d5920d61dd365eacfd1a40726500e25a3ab516df5a1d59a7a9d79ce02db7a2145801b6af5df2c41c95e80b49a39db83d27fd7ff3cf88ba0e6a328d SHA512 4e7c01022d9edf48a0e0dcffcbccf34812f236d1b581760ac115c323de5779fb6212eb4ad7d1953811930a6137cc8f5f59028c73d645d1ca5fb6118dd846ad57 diff --git a/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch b/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch new file mode 100644 index 000000000000..b3d11bbbe7aa --- /dev/null +++ b/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch @@ -0,0 +1,29 @@ +--- a/Build.PL ++++ b/Build.PL +@@ -125,7 +125,7 @@ + + my $hts_lib = "$root"; + my $hts_include = "$root/htslib"; +- if (-f "$hts_lib/libhts.a" && -f "$hts_include/hts.h") { ++ if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") { + $self->config_data('hts_lib' => $hts_lib); + $self->config_data('hts_include' => $hts_include); + return 1; +@@ -145,7 +145,7 @@ + + my $hts_lib = "$root/lib"; + my $hts_include = "$root/include/htslib"; +- if (-f "$hts_lib/libhts.a" && -f "$hts_include/hts.h") { ++ if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") { + $self->config_data('hts_lib' => $hts_lib); + $self->config_data('hts_include' => $hts_include); + return 1; +@@ -164,7 +164,7 @@ + This module requires htslib (http://htslib/org) + Install it if you have not done so already. + +-This script will attempt to locate htslib by looking for hts.h and libhts.a in: ++This script will attempt to locate htslib by looking for hts.h and libhts.so/libhts.a in: + + 1. --htslib command line argument + 2. HTSLIB_DIR environment variable diff --git a/dev-perl/Bio-DB-HTS/metadata.xml b/dev-perl/Bio-DB-HTS/metadata.xml new file mode 100644 index 000000000000..95abbb699ad4 --- /dev/null +++ b/dev-perl/Bio-DB-HTS/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>marecki@gentoo.org</email> + <name>Marek Szuba</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">Ensembl/Bio-DB-HTS</remote-id> + <remote-id type="cpan">Bio-DB-HTS</remote-id> + <remote-id type="cpan-module">Bio::DB::HTS</remote-id> + </upstream> +</pkgmetadata> |