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commit: 9a9cafec65f1eb3de700a077dae30537993823cc |
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Author: Marek Szuba <marecki <AT> gentoo <DOT> org> |
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AuthorDate: Thu Apr 26 11:25:15 2018 +0000 |
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Commit: Marek Szuba <marecki <AT> gentoo <DOT> org> |
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CommitDate: Thu Apr 26 11:30:28 2018 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9a9cafec |
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|
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dev-perl/Bio-DB-HTS: new package |
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|
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Perl bindings for sci-libs/htslib, used by e.g. Ensembl. |
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|
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Package-Manager: Portage-2.3.24, Repoman-2.3.6 |
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|
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dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild | 30 ++++++++++++++++++++++ |
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dev-perl/Bio-DB-HTS/Manifest | 1 + |
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.../files/2.10-build_search_for_so.patch | 29 +++++++++++++++++++++ |
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dev-perl/Bio-DB-HTS/metadata.xml | 17 ++++++++++++ |
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4 files changed, 77 insertions(+) |
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|
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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 |
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new file mode 100644 |
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index 00000000000..02c38cd34f3 |
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--- /dev/null |
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+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild |
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@@ -0,0 +1,30 @@ |
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+# Copyright 1999-2018 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=AVULLO |
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+DIST_VERSION=2.10 |
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+ |
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+inherit perl-module |
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+ |
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+DESCRIPTION="Perl bindings for sci-libs/htslib" |
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+ |
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+LICENSE="Apache-2.0" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="test" |
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+ |
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+RDEPEND="sci-libs/htslib:=" |
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+DEPEND="${RDEPEND} |
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+ dev-perl/Module-Build |
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+ test? ( dev-perl/Test-LeakTrace )" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}/2.10-build_search_for_so.patch" |
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+) |
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+ |
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+src_configure() { |
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+ local myconf="--htslib=${EPREFIX}/usr" |
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+ perl-module_src_configure |
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+} |
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|
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diff --git a/dev-perl/Bio-DB-HTS/Manifest b/dev-perl/Bio-DB-HTS/Manifest |
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new file mode 100644 |
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index 00000000000..536315137fa |
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--- /dev/null |
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+++ b/dev-perl/Bio-DB-HTS/Manifest |
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@@ -0,0 +1 @@ |
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+DIST Bio-DB-HTS-2.10.tar.gz 5245650 BLAKE2B a52d9b1e19d5920d61dd365eacfd1a40726500e25a3ab516df5a1d59a7a9d79ce02db7a2145801b6af5df2c41c95e80b49a39db83d27fd7ff3cf88ba0e6a328d SHA512 4e7c01022d9edf48a0e0dcffcbccf34812f236d1b581760ac115c323de5779fb6212eb4ad7d1953811930a6137cc8f5f59028c73d645d1ca5fb6118dd846ad57 |
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|
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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 |
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new file mode 100644 |
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index 00000000000..b3d11bbbe7a |
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--- /dev/null |
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+++ b/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch |
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@@ -0,0 +1,29 @@ |
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+--- a/Build.PL |
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++++ b/Build.PL |
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+@@ -125,7 +125,7 @@ |
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+ |
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+ my $hts_lib = "$root"; |
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+ my $hts_include = "$root/htslib"; |
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+- if (-f "$hts_lib/libhts.a" && -f "$hts_include/hts.h") { |
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++ if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") { |
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+ $self->config_data('hts_lib' => $hts_lib); |
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+ $self->config_data('hts_include' => $hts_include); |
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+ return 1; |
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+@@ -145,7 +145,7 @@ |
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+ |
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+ my $hts_lib = "$root/lib"; |
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+ my $hts_include = "$root/include/htslib"; |
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+- if (-f "$hts_lib/libhts.a" && -f "$hts_include/hts.h") { |
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++ if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") { |
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+ $self->config_data('hts_lib' => $hts_lib); |
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+ $self->config_data('hts_include' => $hts_include); |
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+ return 1; |
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+@@ -164,7 +164,7 @@ |
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+ This module requires htslib (http://htslib/org) |
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+ Install it if you have not done so already. |
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+ |
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+-This script will attempt to locate htslib by looking for hts.h and libhts.a in: |
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++This script will attempt to locate htslib by looking for hts.h and libhts.so/libhts.a in: |
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+ |
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+ 1. --htslib command line argument |
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+ 2. HTSLIB_DIR environment variable |
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|
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diff --git a/dev-perl/Bio-DB-HTS/metadata.xml b/dev-perl/Bio-DB-HTS/metadata.xml |
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new file mode 100644 |
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index 00000000000..95abbb699ad |
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--- /dev/null |
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+++ b/dev-perl/Bio-DB-HTS/metadata.xml |
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@@ -0,0 +1,17 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <maintainer type="person"> |
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+ <email>marecki@g.o</email> |
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+ <name>Marek Szuba</name> |
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+ </maintainer> |
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+ <maintainer type="project"> |
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+ <email>sci-biology@g.o</email> |
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+ <name>Gentoo Biology Project</name> |
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+ </maintainer> |
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+ <upstream> |
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+ <remote-id type="github">Ensembl/Bio-DB-HTS</remote-id> |
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+ <remote-id type="cpan">Bio-DB-HTS</remote-id> |
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+ <remote-id type="cpan-module">Bio::DB::HTS</remote-id> |
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+ </upstream> |
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+</pkgmetadata> |
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