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sci-biology/bcftools: Remove old
Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
This commit is contained in:
David Seifert
@@ -1,3 +1 @@
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DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e SHA512 f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300
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DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233
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DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed SHA512 fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c
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@@ -1,45 +0,0 @@
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# Copyright 1999-2017 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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EAPI=6
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PYTHON_COMPAT=( python2_7 )
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inherit python-r1
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DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
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HOMEPAGE="http://www.htslib.org"
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SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
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LICENSE="MIT"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE=""
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REQUIRED_USE="${PYTHON_REQUIRED_USE}"
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RDEPEND="
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dev-lang/perl
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=sci-libs/htslib-${PV}*:=
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sys-libs/zlib
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${PYTHON_DEPS}"
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DEPEND="${RDEPEND}"
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PATCHES=(
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"${FILESDIR}"/${PN}-1.5-buildsystem.patch
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"${FILESDIR}"/${PN}-1.5-fix-shebangs.patch
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)
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src_prepare() {
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default
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# remove bundled htslib
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rm -r htslib-* || die
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}
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src_configure() {
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econf \
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--disable-bcftools-plugins \
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--disable-libgsl \
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--disable-configure-htslib \
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--with-htslib=system
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}
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@@ -1,49 +0,0 @@
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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python3_{6,7} )
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inherit python-single-r1
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DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
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HOMEPAGE="http://www.htslib.org"
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SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
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LICENSE="MIT"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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REQUIRED_USE="${PYTHON_REQUIRED_USE}"
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RDEPEND="
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dev-lang/perl
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$(python_gen_cond_dep '
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dev-python/matplotlib[${PYTHON_MULTI_USEDEP}]
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')
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=sci-libs/htslib-${PV}*:=
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sys-libs/zlib:=
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${PYTHON_DEPS}"
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DEPEND="${RDEPEND}"
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PATCHES=(
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"${FILESDIR}"/${PN}-1.9-buildsystem.patch
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"${FILESDIR}"/${PN}-1.9-fix-shebangs.patch
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)
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src_prepare() {
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default
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python_fix_shebang misc/{guess-ploidy,plot-roh}.py
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# remove bundled htslib
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rm -r htslib-* || die
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}
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src_configure() {
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econf \
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--disable-bcftools-plugins \
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--disable-libgsl \
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--disable-configure-htslib \
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--with-htslib=system
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}
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@@ -1,10 +0,0 @@
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--- a/Makefile
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+++ b/Makefile
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@@ -275,7 +275,6 @@
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$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
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$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
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$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
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- $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
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clean: testclean clean-plugins
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-rm -f gmon.out *.o *~ $(PROG) version.h plugins/*.so plugins/*.P
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@@ -1,24 +0,0 @@
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--- a/misc/guess-ploidy.py
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+++ b/misc/guess-ploidy.py
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@@ -1,4 +1,4 @@
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-#!/usr/bin/env python
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+#!/usr/bin/env python2.7
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#
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# Plot the output of "bcftools +guess-ploidy -v"
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#
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--- a/misc/plot-roh.py
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+++ b/misc/plot-roh.py
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@@ -1,4 +1,4 @@
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-#!/usr/bin/python
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+#!/usr/bin/env python2.7
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import glob, gzip, csv, sys, os, copy, re
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csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE)
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--- a/misc/vcfutils.pl
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+++ b/misc/vcfutils.pl
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@@ -1,4 +1,4 @@
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-#!/usr/bin/perl -w
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+#!/usr/bin/env perl
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#
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# Copyright (C) 2010 Broad Institute.
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# Copyright (C) 2011, 2014 Genome Research Ltd.
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@@ -1,10 +0,0 @@
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--- a/Makefile
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+++ b/Makefile
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@@ -282,7 +282,6 @@
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$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
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$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
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$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
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- $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
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clean: testclean clean-plugins
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-rm -f gmon.out *.o *~ $(PROGRAMS) version.h plugins/*.so plugins/*.P
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@@ -1,8 +0,0 @@
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--- a/misc/vcfutils.pl
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+++ b/misc/vcfutils.pl
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@@ -1,4 +1,4 @@
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-#!/usr/bin/perl -w
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+#!/usr/bin/env perl
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#
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# Copyright (C) 2010 Broad Institute.
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# Copyright (C) 2011, 2014 Genome Research Ltd.
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