gentoo resync : 25.08.2020

7 files changed, 3 insertions, 112 deletions

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index c247c7af050a..2dc014f78dfe 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,9 +1,3 @@
-AUX bcftools-1.5-buildsystem.patch 376 BLAKE2B 384bf91c3af4f98c76c0ab6fecdfe0ec9483b77c54517df0ad2703441def7a7a6982ee792ae1775414ab8cec43d0e65ff6d2187be7cb85bb42eb5af8f9b7283e SHA512 c8ede2be5205ab287843662e7b97ecae8d4fc7d2aaf09e0b9fa67f5a3168149b15457e73c2c9d8b74fcfada08ec5c1bbe61013a2ef434ee50acf56eccabf6723
-AUX bcftools-1.5-fix-shebangs.patch 594 BLAKE2B 28d0a58627dcc1b1eb8f546c73a88f76e3277c82772f8a7af814d9ff3bcb116751b065166661c486e8c6b1708a54de227a5ef65d18a8527b38f5119d744539d2 SHA512 e00cc0de35ad5866f7321408a7995f054f80e37e642b6c3097c5e786635dc61baefa7ea8847f2222d32196825e3e44209d63fdfd219c54b09421a4bb310067f5
-AUX bcftools-1.9-buildsystem.patch 380 BLAKE2B b71567ad14d96b85bf449db473b38cd9ff2a32420d9c4d1b606cad0e09a478fd0946b589c62405aceacf234db7abde3fcf180eed7fbf0d8db73565b4424f86b8 SHA512 f0124734e6309eda73e5f32a9832e8c35de1929c6503627564346f097415bc76294371eda1886100ce2f1ed8e0de695e978a720dd4517e8411dcd041797af2b5
-AUX bcftools-1.9-fix-shebangs.patch 198 BLAKE2B 9d6c365c7193c7815216be4f8034c00e0048f7352e15ee24b4359828bf0906755ab9524fb10ad185754652b74007dc2c756b2260f64a263f696cf0f737ff25d7 SHA512 65eecc5e0d5cf3df1538b078c7606b38451e13f4f359ecf9287a9e03721c7c7ba1cd8bd517a98dd34842db22624fbdc570e9707d13f2e2fb82b16b3ca41ca71e
-DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233
-DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed SHA512 fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c
-EBUILD bcftools-1.5.ebuild 868 BLAKE2B acfd6758e27cb9ade023d91074724affd0fa3016af565c809819fae615be61ca8af90edf6b38eaf0a4ed5f3e9eaaa19451096b8d7c27a58c6ed0540bf7260784 SHA512 e0aacba5fc54cbf7a8d64db84e52f28baf8df36fa01c63fc167998c6ec5ef65a040c0725f445970f32888ae947b89d50d92dc2fc704fdf63a8a900762ec367e6
-EBUILD bcftools-1.9-r2.ebuild 1000 BLAKE2B eb5e7bb5f33f5ef22594eb241f3900ee6a6c125cb83b0e425732fbd6d781dac382b1664281e3256587ea8f344db578c1ec778ac2d5ae4794fa67931468cb580c SHA512 90d56585baae31be060fc8a54de5d86c1bd015da187d86a37ceee1176a685a864214e124770dfb895d568bb57e143f9a35b7f627f36598dbf4cb544119f2185d
+DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e SHA512 f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300
+EBUILD bcftools-1.10.2.ebuild 870 BLAKE2B 2368cbe0d749a1214a8f1ad659bc3ea9b51b34c7c45b88e13d8c79eb6919ffcdd73a18e0a1119c5e92781cd79aa184360a9b0fd4187beebaed66ac89d934396f SHA512 9888597c6bd9412688c8375962e9f8a1c4722ca905f57b1d7c729e433ee353b3956fddf397fe65f0f8523f8e588062f02267ec9024bf6c8c3858cd9fa183916a
 MISC metadata.xml 343 BLAKE2B e1664c6d67ebde81b9f99b69d442e0b16891ecd392fddd55ed2aaa885dcb2f4ca39cd627cd3f6367f39b13e35eb1141119e53756d6efc4ac62c819ab1d611633 SHA512 cfa167a5733f40d7e36e9e229229acd883ba7bfd812afb9060c742c505354b1c754070e2e897a48d7611a123b9606b6f43a0816c089e71bf64f3d0dbd8b7184d
diff --git a/sci-biology/bcftools/bcftools-1.9-r2.ebuild b/sci-biology/bcftools/bcftools-1.10.2.ebuild
index 0963c692fcd6..179f7dea77e4 100644
--- a/sci-biology/bcftools/bcftools-1.9-r2.ebuild
+++ b/sci-biology/bcftools/bcftools-1.10.2.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6,7} )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit python-single-r1
 
@@ -26,11 +26,6 @@ RDEPEND="
 	${PYTHON_DEPS}"
 DEPEND="${RDEPEND}"
 
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.9-buildsystem.patch
-	"${FILESDIR}"/${PN}-1.9-fix-shebangs.patch
-)
-
 src_prepare() {
 	default
 
@@ -44,6 +39,5 @@ src_configure() {
 	econf \
 		--disable-bcftools-plugins \
 		--disable-libgsl \
-		--disable-configure-htslib \
 		--with-htslib=system
 }
diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild b/sci-biology/bcftools/bcftools-1.5.ebuild
deleted file mode 100644
index 9b5df1130999..000000000000
--- 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/files/bcftools-1.5-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch
deleted file mode 100644
index 304fc03e7441..000000000000
--- 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 c6cfc8b991d3..000000000000
--- 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 a0df4b917bcb..000000000000
--- 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 76610187c493..000000000000
--- 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.