diff options
Diffstat (limited to 'dev-perl/Bio-DB-HTS')
| -rw-r--r-- | dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.11.ebuild | 31 | ||||
| -rw-r--r-- | dev-perl/Bio-DB-HTS/Manifest | 4 | ||||
| -rw-r--r-- | dev-perl/Bio-DB-HTS/files/2.11-build_split_htslib_opts.patch | 65 | ||||
| -rw-r--r-- | dev-perl/Bio-DB-HTS/metadata.xml | 17 |
4 files changed, 117 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 new file mode 100644 index 000000000000..c82f5a3486d0 --- /dev/null +++ b/dev-perl/Bio-DB-HTS/Manifest @@ -0,0 +1,4 @@ +AUX 2.11-build_split_htslib_opts.patch 2453 BLAKE2B 19f99d0a56db7c4778bc478cd952062e8095997fe9028b6c7e251e2391f9f074774bdaec6db7c610488a921a73abf83edeee2b5f5a5185d4bb422c5dff6a8634 SHA512 4770ebb1bf8fdc3e51f4a020db1c45befa64478bd2cf2d77397e5e7ac09d34d17457ecd2be2fd53062ada48f579621cb959c245493906b9c04367142b27a2fa8 +DIST Bio-DB-HTS-2.11.tar.gz 5250814 BLAKE2B d77ccacebf339a33ab106b997139cdbf79f6c28269a832305e660b28370aca82b4c9824773acdbf8f59b18dd61f40346a9870578dba7b5b989b0f3bc9ad14b35 SHA512 114d90fe92b684250183b45b4d23d2dd45ecdcb2fa54f7b1c311ed668d8e87953adb861f709a0a48ff2b873ce777b21bc3b557bafa0df216b9a71b59facff6fd +EBUILD Bio-DB-HTS-2.11.ebuild 639 BLAKE2B 9761dddc9216bc11e3a167d067b6d33fc4a8f7b7aeaf690a02c3816620bc10fd9a6d306def470dd056de0958538433a784a62328f48aa4447b7c437460881c44 SHA512 789ad5439ac7014585b61ac11790fff6c6786fb5c249a7e895fcc6c7a988e4f61e097d98883cb36203e0ab030fc874f38dfbd969e0a3b6c9c6a61a33b90f3e9e +MISC metadata.xml 555 BLAKE2B fe8d2547a6d959f24231c15b5803e8e71dd94ac0d865dd0a53dff97c62b39db8ff40f845f7d4a48cd4dc19d31c044e06ca8394d745a79c532fc61e96a66dab3f SHA512 9e03a79d88ca855783562bd5d3b9a4f71698c2caae43c009bbcf312bd5810d362842cb4e834291b08a5231785f59fc5598edca6868716d5a7487716d10acac39 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 + 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> |