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commit: 4f1be5045ba43a9e9596d89ab2d47e50880f6537 |
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Author: Marek Szuba <marecki <AT> gentoo <DOT> org> |
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AuthorDate: Tue May 1 13:11:29 2018 +0000 |
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Commit: Marek Szuba <marecki <AT> gentoo <DOT> org> |
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CommitDate: Tue May 1 13:12:08 2018 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4f1be504 |
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|
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dev-perl/Bio-DB-HTS: bump to 2.11 |
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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-2.11.ebuild | 31 +++++++++++ |
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dev-perl/Bio-DB-HTS/Manifest | 1 + |
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.../files/2.11-build_split_htslib_opts.patch | 65 ++++++++++++++++++++++ |
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3 files changed, 97 insertions(+) |
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|
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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 |
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new file mode 100644 |
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index 00000000000..e5c23d67da0 |
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--- /dev/null |
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+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.11.ebuild |
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@@ -0,0 +1,31 @@ |
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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=2.11 |
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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-biology/bioperl |
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+ 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}/2.11-build_split_htslib_opts.patch" |
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+) |
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+ |
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+src_configure() { |
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+ local myconf="--htslib-includedir=${EPREFIX}/usr/include/htslib --htslib-libdir=${EPREFIX}/usr/$(get_libdir)" |
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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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index 536315137fa..6770bf66986 100644 |
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--- a/dev-perl/Bio-DB-HTS/Manifest |
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+++ b/dev-perl/Bio-DB-HTS/Manifest |
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@@ -1 +1,2 @@ |
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DIST Bio-DB-HTS-2.10.tar.gz 5245650 BLAKE2B a52d9b1e19d5920d61dd365eacfd1a40726500e25a3ab516df5a1d59a7a9d79ce02db7a2145801b6af5df2c41c95e80b49a39db83d27fd7ff3cf88ba0e6a328d SHA512 4e7c01022d9edf48a0e0dcffcbccf34812f236d1b581760ac115c323de5779fb6212eb4ad7d1953811930a6137cc8f5f59028c73d645d1ca5fb6118dd846ad57 |
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+DIST Bio-DB-HTS-2.11.tar.gz 5250814 BLAKE2B d77ccacebf339a33ab106b997139cdbf79f6c28269a832305e660b28370aca82b4c9824773acdbf8f59b18dd61f40346a9870578dba7b5b989b0f3bc9ad14b35 SHA512 114d90fe92b684250183b45b4d23d2dd45ecdcb2fa54f7b1c311ed668d8e87953adb861f709a0a48ff2b873ce777b21bc3b557bafa0df216b9a71b59facff6fd |
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|
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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 |
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new file mode 100644 |
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index 00000000000..727c500360d |
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--- /dev/null |
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+++ b/dev-perl/Bio-DB-HTS/files/2.11-build_split_htslib_opts.patch |
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@@ -0,0 +1,65 @@ |
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+diff --git a/Build.PL b/Build.PL |
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+index 0d684b7..87a223b 100644 |
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+--- a/Build.PL |
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++++ b/Build.PL |
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+@@ -68,7 +68,15 @@ sub find_hts { |
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+ # If either of these are set, we expect to find the htslib files there: |
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+ # (They're explicitly set by the user, so we shouldn't fall back to |
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+ # finding another copy somewhere else.) |
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+- if (my $dir = $self->args('htslib')) { |
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++ my $incdir = $self->args('htslib-includedir'); |
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++ my $libdir = $self->args('htslib-libdir'); |
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++ if ($incdir && $libdir) { |
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++ return 1 if $self->find_hts_in_split_install_dirs($incdir, $libdir); |
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++ $self->die_hts_not_found( |
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++ "--htslib-includedir '$incdir' or --htslib-libdir '$libdir' command line parameters do not contain expected files\n" |
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++ ); |
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++ } |
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++ elsif (my $dir = $self->args('htslib')) { |
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+ return 1 if $self->find_hts_in_build_dir($dir); |
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+ return 1 if $self->find_hts_in_install_dir($dir); |
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+ $self->die_hts_not_found( |
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+@@ -158,6 +166,23 @@ sub find_hts_in_install_dir { |
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+ } |
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+ } |
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+ |
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++sub find_hts_in_split_install_dirs { |
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++ my ($self, $hts_include, $hts_lib) = @_; |
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++ |
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++ chomp($hts_lib); |
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++ chomp($hts_include); |
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++ $hts_include =~ s{include/htslib$}{include}; |
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++ |
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++ if (hts_dev_files_exist($hts_lib, $hts_include)) { |
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++ $self->config_data('hts_lib' => $hts_lib); |
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++ $self->config_data('hts_include' => $hts_include); |
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++ return 1; |
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++ } |
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++ else { |
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++ return 0; |
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++ } |
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++} |
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++ |
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+ sub die_hts_not_found { |
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+ my ($self, $msg) = @_; |
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+ |
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+@@ -170,12 +195,13 @@ Install it if you have not done so already. |
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+ This script will attempt to locate HTSlib by looking for htslib/hts.h |
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+ and libhts.a / libhts.so 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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+- 3. --prefix command line argument (which also sets installation location) |
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+- 4. Alien::HTSlib dependency resolver |
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+- 5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable) |
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+- 6. common library locations: /usr /usr/local, /usr/share, /opt/local |
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++ 1. --htslib-includedir and --htslib-libdir command line arguments |
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++ 2. --htslib command line argument |
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++ 3. HTSLIB_DIR environment variable |
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++ 4. --prefix command line argument (which also sets installation location) |
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++ 5. Alien::HTSlib dependency resolver |
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++ 6. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable) |
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++ 7. common library locations: /usr /usr/local, /usr/share, /opt/local |
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+ |
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+ END |
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+ |