commit: 5fa92ad679d028ae8e8b88fc044bbbacd475780d Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Aug 3 21:11:15 2020 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Aug 3 21:11:15 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5fa92ad6
sci-biology/bcftools: Remove old Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/bcftools/Manifest | 2 - sci-biology/bcftools/bcftools-1.5.ebuild | 45 -------------------- sci-biology/bcftools/bcftools-1.9-r2.ebuild | 49 ---------------------- .../bcftools/files/bcftools-1.5-buildsystem.patch | 10 ----- .../bcftools/files/bcftools-1.5-fix-shebangs.patch | 24 ----------- .../bcftools/files/bcftools-1.9-buildsystem.patch | 10 ----- .../bcftools/files/bcftools-1.9-fix-shebangs.patch | 8 ---- 7 files changed, 148 deletions(-) diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index 508a5c41fe3..77114df86c0 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1,3 +1 @@ DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e SHA512 f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300 -DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233 -DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed SHA512 fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild b/sci-biology/bcftools/bcftools-1.5.ebuild deleted file mode 100644 index 9b5df113099..00000000000 --- a/sci-biology/bcftools/bcftools-1.5.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit python-r1 - -DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" -HOMEPAGE="http://www.htslib.org"; -SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"; - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - dev-lang/perl - =sci-libs/htslib-${PV}*:= - sys-libs/zlib - ${PYTHON_DEPS}" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-1.5-buildsystem.patch - "${FILESDIR}"/${PN}-1.5-fix-shebangs.patch -) - -src_prepare() { - default - - # remove bundled htslib - rm -r htslib-* || die -} - -src_configure() { - econf \ - --disable-bcftools-plugins \ - --disable-libgsl \ - --disable-configure-htslib \ - --with-htslib=system -} diff --git a/sci-biology/bcftools/bcftools-1.9-r2.ebuild b/sci-biology/bcftools/bcftools-1.9-r2.ebuild deleted file mode 100644 index 0963c692fcd..00000000000 --- a/sci-biology/bcftools/bcftools-1.9-r2.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{6,7} ) - -inherit python-single-r1 - -DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" -HOMEPAGE="http://www.htslib.org"; -SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"; - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - dev-lang/perl - $(python_gen_cond_dep ' - dev-python/matplotlib[${PYTHON_MULTI_USEDEP}] - ') - =sci-libs/htslib-${PV}*:= - sys-libs/zlib:= - ${PYTHON_DEPS}" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-1.9-buildsystem.patch - "${FILESDIR}"/${PN}-1.9-fix-shebangs.patch -) - -src_prepare() { - default - - python_fix_shebang misc/{guess-ploidy,plot-roh}.py - - # remove bundled htslib - rm -r htslib-* || die -} - -src_configure() { - econf \ - --disable-bcftools-plugins \ - --disable-libgsl \ - --disable-configure-htslib \ - --with-htslib=system -} diff --git a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch deleted file mode 100644 index 304fc03e744..00000000000 --- a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/Makefile -+++ b/Makefile -@@ -275,7 +275,6 @@ - $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) - $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) - $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) -- $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir) - - clean: testclean clean-plugins - -rm -f gmon.out *.o *~ $(PROG) version.h plugins/*.so plugins/*.P diff --git a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch deleted file mode 100644 index c6cfc8b991d..00000000000 --- a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- a/misc/guess-ploidy.py -+++ b/misc/guess-ploidy.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python2.7 - # - # Plot the output of "bcftools +guess-ploidy -v" - # ---- a/misc/plot-roh.py -+++ b/misc/plot-roh.py -@@ -1,4 +1,4 @@ --#!/usr/bin/python -+#!/usr/bin/env python2.7 - - import glob, gzip, csv, sys, os, copy, re - csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE) ---- a/misc/vcfutils.pl -+++ b/misc/vcfutils.pl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Copyright (C) 2010 Broad Institute. - # Copyright (C) 2011, 2014 Genome Research Ltd. diff --git a/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch deleted file mode 100644 index a0df4b917bc..00000000000 --- a/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/Makefile -+++ b/Makefile -@@ -282,7 +282,6 @@ - $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) - $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) - $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) -- $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir) - - clean: testclean clean-plugins - -rm -f gmon.out *.o *~ $(PROGRAMS) version.h plugins/*.so plugins/*.P diff --git a/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch deleted file mode 100644 index 76610187c49..00000000000 --- a/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch +++ /dev/null @@ -1,8 +0,0 @@ ---- a/misc/vcfutils.pl -+++ b/misc/vcfutils.pl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Copyright (C) 2010 Broad Institute. - # Copyright (C) 2011, 2014 Genome Research Ltd.
