[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/files/, sci-biology/bcftools/

[David Seifert]

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.