From 2f51c9978dda4c6e8debca43e4235ecc86914032 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 25 Dec 2017 17:37:52 +0000 Subject: gentoo resync : 25.12.2017 --- sci-biology/bowtie/Manifest | 3 -- sci-biology/bowtie/bowtie-1.1.2.ebuild | 54 ------------------------------ sci-biology/bowtie/bowtie-2.2.6.ebuild | 60 ---------------------------------- 3 files changed, 117 deletions(-) delete mode 100644 sci-biology/bowtie/bowtie-1.1.2.ebuild delete mode 100644 sci-biology/bowtie/bowtie-2.2.6.ebuild (limited to 'sci-biology/bowtie') diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index c72595263210..bbf916477036 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -8,10 +8,7 @@ AUX bowtie-1.1.2-tbb-tinythread-missing.patch 554 BLAKE2B 745629aa93f2e74191b944 AUX bowtie-1.1.2-unbundle-seqan.patch 751 BLAKE2B d9689b298f21f4619dbbed96b58d8ae7fc5f646539ae33291222d282153b545ad6fb3e30fe1ba5f0f452e2f3e7e9706b6761f5d4184dcd5ad96a55ccc7b246be SHA512 9a68ccc98774a2c9ddb8f45b5ed009230d14d3e29837c6dd8aac34e298f57208361ef45d0e7d9d074495f3465b58f08606cced9e4fccb549785591ff954cb2b8 AUX bowtie-2.2.9-fix-c++14.patch 687 BLAKE2B a75f473f429379789a97142d7820fb19fc1a64b764236c6fa1c068cefb03e37a58b41b0a515a62d42e85b3131f0dfe8f2bb856126528099277394674a0e53248 SHA512 3aa6e7a30fdf93ae564091ce9b87338ab9feccbd0c873f4130af71dc94fd3b27527b42a93f13471a2613bad44dbacd639d17515000f03856695a0021ce14dfc5 DIST bowtie-1.1.2-src.zip 7713258 BLAKE2B ac10aca905099b5a70d3fab6f90e2dc4713bf7b460d027abf89a6ef6103979724e70b2915a86ffa571b59dcd9df768c80be1846cccd08f7f85dd402ce64c0cb0 SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 -DIST bowtie2-2.2.6-source.zip 5728779 BLAKE2B acd821376755e6bebfd58c39012a370b1aadf4cf8c52eafa1c648c93a0cab695c9c37761498260ed709bc25eb0b671797ff1c74da9787d616c8c39d1296a37eb SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205 EBUILD bowtie-1.1.2-r1.ebuild 1643 BLAKE2B 81f79b8b8d9b9a56061bf92df193a21e2db03bdacb6290020e8fb2426e3e1cf9e5a6a802cb6fa5f5f68be8d7f92f749e14c0c3528ebad5825d3927bcf33ca483 SHA512 8b5c22f29aafb5977313ea002fcd654ac991015f7808f02f8e02c2105dd9a6fa77b5f5342e82d38b07674c93dbe397333be78f6d1ca9a24a60531d6a40efe382 -EBUILD bowtie-1.1.2.ebuild 1058 BLAKE2B 4aae2773c629826866242b9c62f08e904d70f55b5094b46f727ae59d0fe75845ad3c809cde724753f0ada493294340e59a2290960f6049f3795d4352b9ca4a6a SHA512 33bd306019d37f3eb05922805e7035bf82bd40c21934c541bd6c56522afc1aa2ebfa900024d72cd0555e290560de07b1adadb98673100b934f53779c2e40376f -EBUILD bowtie-2.2.6.ebuild 1230 BLAKE2B 0382c42265c5fd5192d8d177f91f803fd4f9b28f107bcffed14573386c283d59e77d6ca72872f1c86c5f8a79f05263257865a39cfac64a8d4d6c77acb2aa299b SHA512 7c1546de18fa549defa619877688e38b2e90a5875ac9d6ca2728ae7788e495870efbbafeaabe0e3a79788e393e8d273b715fd9bcfef4267ac5daba1dd18a87ff EBUILD bowtie-2.2.9.ebuild 1277 BLAKE2B b9cf9edc34af3f01eb1cde1510637bbcbaf7206d9a24135d859d14dcefe793abd0b78dd19dbcd1835840514e754061aee86a79d5992ca68d316c64c98bb4891c SHA512 40e22698d5df241b8b98c601f8ed22276d39f4c9818bb23afec0a39b625fd38a0fdb3f4b4d6f8c01b458e2b6b3464a7ee8a135bd446f3488354eeca9934daa85 MISC metadata.xml 528 BLAKE2B 310fb406a0dbe56b194ae13cf521264e105f9d849b09e10d5d7e556c7d00a9cc7a0f9546a91e43f30344c9ec14a76e0d8a3f037fb4cb91bba68999d9f45b69e0 SHA512 1eb83cbd7d7e747bc94021051ba6ae0bf22411091287b754851a9f6824b263b6ca83c9a0d055c0b6ab24963ceea9b32d76bf1b343f48a3ee4bd322fec539b301 diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild deleted file mode 100644 index 1ada8a0fdc2b..000000000000 --- a/sci-biology/bowtie/bowtie-1.1.2.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/" -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="amd64 x86 ~x64-macos" - -IUSE="examples +tbb" - -DEPEND="app-arch/unzip - tbb? ( dev-cpp/tbb )" -RDEPEND="" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -src_prepare() { - # always include tinythread.cpp - epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch" -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -} diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild deleted file mode 100644 index 29826473a3b3..000000000000 --- a/sci-biology/bowtie/bowtie-2.2.6.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" - -LICENSE="GPL-3" -SLOT="2" -KEYWORDS="amd64 x86" - -IUSE="examples cpu_flags_x86_sse2 +tbb" - -RDEPEND="dev-lang/perl" -DEPEND="${RDEPEND} - app-arch/unzip - tbb? ( dev-cpp/tbb )" - -S="${WORKDIR}/${PN}2-${PV}" - -DOCS=( AUTHORS NEWS TUTORIAL ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -pkg_pretend() { - if ! use cpu_flags_x86_sse2 ; then - eerror "This package requires a CPU supporting the SSE2 instruction set." - die "SSE2 support missing" - fi -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS} -msse2" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN}2 ${PN}2-* - - exeinto /usr/libexec/${PN}2 - doexe scripts/* - - newman MANUAL ${PN}2.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN}2 - doins -r example - fi -} -- cgit v1.2.3