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Sun, 28 Oct 2018 20:25:03 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1540758277.18d496c1b4022e892aae9fcf3350b302b34357ed.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/samtools/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/samtools/Manifest sci-biology/samtools/samtools-1.9.ebuild X-VCS-Directories: sci-biology/samtools/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 18d496c1b4022e892aae9fcf3350b302b34357ed X-VCS-Branch: master Date: Sun, 28 Oct 2018 20:25:03 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 5168a7dd-de8a-4a65-85c2-8180247cabdb X-Archives-Hash: 1d9b5d08e6a9fef1020e60c7f8bfd707 commit: 18d496c1b4022e892aae9fcf3350b302b34357ed Author: David Seifert gentoo org> AuthorDate: Sun Oct 28 20:24:37 2018 +0000 Commit: David Seifert gentoo org> CommitDate: Sun Oct 28 20:24:37 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=18d496c1 sci-biology/samtools: Version bump to 1.9 Bug: https://bugs.gentoo.org/647714 Signed-off-by: David Seifert gentoo.org> Package-Manager: Portage-2.3.50, Repoman-2.3.11 sci-biology/samtools/Manifest | 1 + sci-biology/samtools/samtools-1.9.ebuild | 52 ++++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+) diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 8269a052050..7ce21379a95 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,2 +1,3 @@ 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 diff --git a/sci-biology/samtools/samtools-1.9.ebuild b/sci-biology/samtools/samtools-1.9.ebuild new file mode 100644 index 00000000000..bdcd115aafe --- /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 +}