From 623ee73d661e5ed8475cb264511f683407d87365 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Sun, 12 Apr 2020 03:41:30 +0100
Subject: gentoo Easter resync : 12.04.2020

---
 sci-biology/samtools/Manifest               |  2 +-
 sci-biology/samtools/samtools-1.9-r1.ebuild | 49 +++++++++++++++++++++++++++
 sci-biology/samtools/samtools-1.9.ebuild    | 52 -----------------------------
 3 files changed, 50 insertions(+), 53 deletions(-)
 create mode 100644 sci-biology/samtools/samtools-1.9-r1.ebuild
 delete mode 100644 sci-biology/samtools/samtools-1.9.ebuild

(limited to 'sci-biology/samtools')

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index cb820df291ac..45ef440561f3 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -5,5 +5,5 @@ DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf58
 DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff SHA512 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f
 EBUILD samtools-0.1.20-r3.ebuild 2363 BLAKE2B 6050d698f26b9962192cdbc6c3729bb812041fc92f4ba4490dc6f50e71c08853d6e2e4c6592c324c3efc3ac0da058e8b254475d6fc788f314798cdcaf85a4fc0 SHA512 f79e0f723d86e7c2060163a3b79e6624ea58d21e7c8ddeb87be40a7972cd97e60df82dacaae23b8a89cec2a0517ffdae8804ac71044685b40d5c5769f8964557
 EBUILD samtools-1.5.ebuild 1107 BLAKE2B 2088a3fcc483de227bd92c80cd9ae2bf0257af773298bebcd077d7b2385eb43a6bfde82c7fadb0e2af3400b825e5b1b3c3c4f633cc7631beb4d0dcbb39cdd2cf SHA512 2f1701695fe3aa270bd75bedc3f847b3057ea1a6d9dca386a8f420df22ab78f51b12c8e1ca80d7d2fb1221d246047a78e914022c8e4c8bae5b0b053f3b130cfd
-EBUILD samtools-1.9.ebuild 954 BLAKE2B 7019d0294f9a78d3957f56a006d0c8a401553c74c27ec14707e1eda401b9f3865089321267e873652ca8b8eff382ecb9777424b06773a4ec661ef5bd1a9267dc SHA512 4129a3ccb8e66aaa1ca1c0557acf76c27225486d1145d07fa372f48939a2c1fc30532964076e65aee5dde97c49e750f1423a0cc644966eabf0f6e54846a3bcfd
+EBUILD samtools-1.9-r1.ebuild 926 BLAKE2B a71ab1165f9fad65f0ff932880a661fb43435ebc1c72839ed8f57d3a1ee8b11d5441d53404ed650d634334a8f197d4275f82831d7332bdbbe6f110506f0d0230 SHA512 f75851ece84f8863c7352fad6133fe66299cfe94561a62f7dd4a2bf9a82d2a2400be483874d109b67b643807a25d6907d47c8310732d4b13577e27af685857bd
 MISC metadata.xml 408 BLAKE2B 28b519bf32b116c92c1a695553637a44815ff1aaf18468a5d2d5ef448d8dd53728aadf7606c6ab53ae6bb21e88fa4a48c7b443e3d0a13a5658592dc0e768ed3c SHA512 8c8d240fd37400e43637e12f008f8f2b03fcca062883dd63ccc6956bbfc46d05709f032d146a95452db35b546ff828239b108b3a331f5295ec97872d6c9478fb
diff --git a/sci-biology/samtools/samtools-1.9-r1.ebuild b/sci-biology/samtools/samtools-1.9-r1.ebuild
new file mode 100644
index 000000000000..0d0f993895fc
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.9-r1.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+RDEPEND="
+	dev-lang/perl
+	=sci-libs/htslib-${PV}*
+	sys-libs/ncurses:0=
+	sys-libs/zlib:="
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+	default
+
+	# remove bundled htslib
+	rm -r htslib-* || die
+
+	eautoreconf
+}
+
+src_test() {
+	local -x LD_LIBRARY_PATH="${S}"
+	default
+}
+
+src_install() {
+	default
+
+	# varfilter.py has been retired upstream for being py2 only
+	rm "${ED}"/usr/bin/varfilter.py || die
+
+	if use examples; then
+		dodoc -r examples
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+}
diff --git a/sci-biology/samtools/samtools-1.9.ebuild b/sci-biology/samtools/samtools-1.9.ebuild
deleted file mode 100644
index bdcd115aafee..000000000000
--- a/sci-biology/samtools/samtools-1.9.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools python-single-r1 toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	dev-lang/perl
-	=sci-libs/htslib-${PV}*
-	sys-libs/ncurses:0=
-	sys-libs/zlib:=
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare() {
-	default
-
-	python_fix_shebang misc/varfilter.py
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-
-	eautoreconf
-}
-
-src_test() {
-	local -x LD_LIBRARY_PATH="${S}"
-	default
-}
-
-src_install() {
-	default
-
-	if use examples; then
-		dodoc -r examples
-		docompress -x /usr/share/doc/${PF}/examples
-	fi
-}
-- 
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