dev-perl/Bio-DB-HTS: bump to 2.11

Package-Manager: Portage-2.3.24, Repoman-2.3.6

3 files changed, 97 insertions, 0 deletions

diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.11.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.11.ebuild
new file mode 100644
index 000000000000..e5c23d67da05
--- /dev/null
+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.11.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DIST_AUTHOR=AVULLO
+DIST_VERSION=2.11
+
+inherit perl-module
+
+DESCRIPTION="Perl bindings for sci-libs/htslib"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="sci-biology/bioperl
+	sci-libs/htslib:="
+DEPEND="${RDEPEND}
+	dev-perl/Module-Build
+	test? ( dev-perl/Test-LeakTrace )"
+
+PATCHES=(
+	"${FILESDIR}/2.11-build_split_htslib_opts.patch"
+)
+
+src_configure() {
+	local myconf="--htslib-includedir=${EPREFIX}/usr/include/htslib --htslib-libdir=${EPREFIX}/usr/$(get_libdir)"
+	perl-module_src_configure
+}
diff --git a/dev-perl/Bio-DB-HTS/Manifest b/dev-perl/Bio-DB-HTS/Manifest
index 536315137fa5..6770bf66986c 100644
--- a/dev-perl/Bio-DB-HTS/Manifest
+++ b/dev-perl/Bio-DB-HTS/Manifest
@@ -1 +1,2 @@
 DIST Bio-DB-HTS-2.10.tar.gz 5245650 BLAKE2B a52d9b1e19d5920d61dd365eacfd1a40726500e25a3ab516df5a1d59a7a9d79ce02db7a2145801b6af5df2c41c95e80b49a39db83d27fd7ff3cf88ba0e6a328d SHA512 4e7c01022d9edf48a0e0dcffcbccf34812f236d1b581760ac115c323de5779fb6212eb4ad7d1953811930a6137cc8f5f59028c73d645d1ca5fb6118dd846ad57
+DIST Bio-DB-HTS-2.11.tar.gz 5250814 BLAKE2B d77ccacebf339a33ab106b997139cdbf79f6c28269a832305e660b28370aca82b4c9824773acdbf8f59b18dd61f40346a9870578dba7b5b989b0f3bc9ad14b35 SHA512 114d90fe92b684250183b45b4d23d2dd45ecdcb2fa54f7b1c311ed668d8e87953adb861f709a0a48ff2b873ce777b21bc3b557bafa0df216b9a71b59facff6fd
diff --git a/dev-perl/Bio-DB-HTS/files/2.11-build_split_htslib_opts.patch b/dev-perl/Bio-DB-HTS/files/2.11-build_split_htslib_opts.patch
new file mode 100644
index 000000000000..727c500360d1
--- /dev/null
+++ b/dev-perl/Bio-DB-HTS/files/2.11-build_split_htslib_opts.patch
@@ -0,0 +1,65 @@
+diff --git a/Build.PL b/Build.PL
+index 0d684b7..87a223b 100644
+--- a/Build.PL
++++ b/Build.PL
+@@ -68,7 +68,15 @@ sub find_hts {
+     # If either of these are set, we expect to find the htslib files there:
+     # (They're explicitly set by the user, so we shouldn't fall back to
+     # finding another copy somewhere else.)
+-    if (my $dir = $self->args('htslib')) {
++    my $incdir = $self->args('htslib-includedir');
++    my $libdir = $self->args('htslib-libdir');
++    if ($incdir && $libdir) {
++        return 1 if $self->find_hts_in_split_install_dirs($incdir, $libdir);
++        $self->die_hts_not_found(
++            "--htslib-includedir '$incdir' or --htslib-libdir '$libdir' command line parameters do not contain expected files\n"
++        );
++    }
++    elsif (my $dir = $self->args('htslib')) {
+         return 1 if $self->find_hts_in_build_dir($dir);
+         return 1 if $self->find_hts_in_install_dir($dir);
+         $self->die_hts_not_found(
+@@ -158,6 +166,23 @@ sub find_hts_in_install_dir {
+     }
+ }
+ 
++sub find_hts_in_split_install_dirs {
++    my ($self, $hts_include, $hts_lib) = @_;
++
++    chomp($hts_lib);
++    chomp($hts_include);
++    $hts_include =~ s{include/htslib$}{include};
++
++    if (hts_dev_files_exist($hts_lib, $hts_include)) {
++        $self->config_data('hts_lib'     => $hts_lib);
++        $self->config_data('hts_include' => $hts_include);
++        return 1;
++    }
++    else {
++        return 0;
++    }
++}
++
+ sub die_hts_not_found {
+     my ($self, $msg) = @_;
+ 
+@@ -170,12 +195,13 @@ Install it if you have not done so already.
+ This script will attempt to locate HTSlib by looking for htslib/hts.h
+ and libhts.a / libhts.so in:
+ 
+-  1. --htslib command line argument
+-  2. HTSLIB_DIR environment variable
+-  3. --prefix command line argument (which also sets installation location)
+-  4. Alien::HTSlib dependency resolver
+-  5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
+-  6. common library locations: /usr /usr/local, /usr/share, /opt/local
++  1. --htslib-includedir and --htslib-libdir command line arguments
++  2. --htslib command line argument
++  3. HTSLIB_DIR environment variable
++  4. --prefix command line argument (which also sets installation location)
++  5. Alien::HTSlib dependency resolver
++  6. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
++  7. common library locations: /usr /usr/local, /usr/share, /opt/local
+ 
+ END
+