commit: a90d776a610fe64027ef7fc4810423b774385ba3
Author: Kent Fredric <kentnl <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 3 13:05:46 2020 +0000
Commit: Kent Fredric <kentnl <AT> gentoo <DOT> org>
CommitDate: Fri Jul 3 14:59:35 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a90d776a
dev-perl/Bio-DB-HTS: -r1 bump for EAPI7 + toolchain love
- EAPI7
- Ensure not breaking when LD=!ccld
- Ensure passing CFLAGS to make/compiler
- Populate more remote-id's in metadata.xml
Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Kent Fredric <kentnl <AT> gentoo.org>
dev-perl/Bio-DB-HTS/Bio-DB-HTS-3.10.0-r1.ebuild | 47 +++++++++++++++++++++++++
dev-perl/Bio-DB-HTS/metadata.xml | 27 ++++++++++++++
2 files changed, 74 insertions(+)
diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-3.10.0-r1.ebuild
b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-3.10.0-r1.ebuild
new file mode 100644
index 00000000000..dcae1156e88
--- /dev/null
+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-3.10.0-r1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DIST_AUTHOR=AVULLO
+DIST_VERSION=3.01
+
+inherit perl-module
+
+DESCRIPTION="Perl bindings for sci-libs/htslib"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ sci-biology/bioperl
+ sci-libs/htslib:=
+"
+DEPEND="
+ dev-perl/Module-Build
+ sci-libs/htslib:=
+"
+BDEPEND="${RDEPEND}
+ dev-perl/Module-Build
+ test? ( dev-perl/Test-LeakTrace )"
+
+PATCHES=(
+ "${FILESDIR}/2.11-build_env_ldflags.patch"
+ "${FILESDIR}/2.11-build_split_htslib_opts.patch"
+)
+
+src_configure() {
+ local myconf="--htslib-includedir=${EPREFIX}/usr/include/htslib
--htslib-libdir=${EPREFIX}/usr/$(get_libdir)"
+ unset LD
+ if [[ -n "${CCLD}" ]]; then
+ export LD="${CCLD}"
+ fi
+ perl-module_src_configure
+}
+src_compile() {
+ ./Build --config optimize="${CFLAGS}" build || die
+}
diff --git a/dev-perl/Bio-DB-HTS/metadata.xml b/dev-perl/Bio-DB-HTS/metadata.xml
index 95abbb699ad..126683a7c28 100644
--- a/dev-perl/Bio-DB-HTS/metadata.xml
+++ b/dev-perl/Bio-DB-HTS/metadata.xml
@@ -13,5 +13,32 @@
<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>
+ <remote-id
type="cpan-module">Bio::DB::HTS::AlignWrapper</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::Alignment</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::Constants</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTS::Fai</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTS::Faidx</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::FetchIterator</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTS::Kseq</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::Kseq::Record</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTS::Pileup</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::PileupWrapper</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTS::Query</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::ReadIterator</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTS::Segment</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::Segment::Iterator</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::SplitAlignmentPart</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTS::Tabix</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::Tabix::Iterator</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTS::Target</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTS::VCF</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::VCF::Header</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::VCF::HeaderPtr</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::VCF::Iterator</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTS::VCF::Row</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::VCF::RowPtr</remote-id>
+ <remote-id
type="cpan-module">Bio::DB::HTS::VCF::Sweep</remote-id>
+ <remote-id type="cpan-module">Bio::DB::HTSfile</remote-id>
+ <remote-id
type="cpan-module">Bio::SeqFeature::HTSCoverage</remote-id>
</upstream>
</pkgmetadata>
