gentoo resync : 03.11.2018

6 files changed, 112 insertions, 0 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 6ba6bf0411ba..7aa57a68ff6a 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 9f7afa61e8c2..2c0602a79c08 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,5 +1,8 @@
 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-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.ebuild 927 BLAKE2B 3e9c712316fa510ddc7be30c398565e3fa4e435fe58cf4263ba3c69dca34b4c227fc80ea23c52e70437a3b9058645f02505a17831c04a23e97086175ed8ee383 SHA512 0cbb0d08596819f7769d23ade97627b6ac9362140904609a2ea0603b8285e94ea2472721a49f298e7aae9a97d3495c3816e8229620a1a11225d2fcd881504cf8
 MISC metadata.xml 452 BLAKE2B 53a356b0569d9db1377bc1881d58b4b354d4861eb21b2c602df59b7923b175a20623cf3369695416eb08d44fabe32036f5a5ec3119c765c8f85347d3b094918a SHA512 eb656430c9ee5ffee5ec5f9f8f3c69e8b0d1ae124cd720ae4af6c3c160da5dc261838744f75e838a85935bbc9bd5201b038ee11cb41a0e1209c9df58aa85fc1a
diff --git a/sci-biology/bcftools/bcftools-1.9.ebuild b/sci-biology/bcftools/bcftools-1.9.ebuild
new file mode 100644
index 000000000000..53e47bc01a81
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.9.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_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}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+REQUIRED_USE="${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}-1.9-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-1.9-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch
new file mode 100644
index 000000000000..76610187c493
--- /dev/null
+++ b/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch
@@ -0,0 +1,8 @@
+--- 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/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
+}