gentoo resync : 03.11.2018

2 files changed, 54 insertions, 0 deletions

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 14a6d41c489e..cb820df291ac 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -2,6 +2,8 @@ AUX samtools-0.1.20-buildsystem.patch 6737 BLAKE2B 71445f57735903bccc2720a32f42b
 AUX samtools-1.5-buildsystem.patch 18442 BLAKE2B df389fd2eb6cfa4fafc987eb8e2e1e5d050a9373305f752516c77f415619f5c5b7ff8e2f8c8fd04769c269f9d385f0130443311d9468a591a4531a9e3127725f SHA512 2405c9c5bd2892756dd70147d0bc57f11f869ac2b6bb12d4350e3f7145727a4c8a602489bca5dbcbe8131d52572d4573e8507a2b989ac0ac86aa8dfef92e58d4
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059
+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
 MISC metadata.xml 408 BLAKE2B 28b519bf32b116c92c1a695553637a44815ff1aaf18468a5d2d5ef448d8dd53728aadf7606c6ab53ae6bb21e88fa4a48c7b443e3d0a13a5658592dc0e768ed3c SHA512 8c8d240fd37400e43637e12f008f8f2b03fcca062883dd63ccc6956bbfc46d05709f032d146a95452db35b546ff828239b108b3a331f5295ec97872d6c9478fb
diff --git a/sci-biology/samtools/samtools-1.9.ebuild b/sci-biology/samtools/samtools-1.9.ebuild
new file mode 100644
index 000000000000..bdcd115aafee
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.9.ebuild
@@ -0,0 +1,52 @@
+# 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
+}