[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/

[Martin Mokrejs]

commit:     51f9e3636c1422b40200dcc11c4122f356cfe4de
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 19 11:24:18 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 19 11:24:18 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=51f9e363

sci-biology/bowtie: removing -9999 ebuild

Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/bowtie/bowtie-9999.ebuild | 81 -----------------------------------
 1 file changed, 81 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-9999.ebuild b/sci-biology/bowtie/bowtie-9999.ebuild
deleted file mode 100644
index d54d0a544..000000000
--- a/sci-biology/bowtie/bowtie-9999.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic toolchain-funcs git-r3
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"
-EGIT_BRANCH="bug_fixes"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS=""
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	sci-biology/seqan:1.4
-	app-arch/unzip"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-PATCHES=( "${FILESDIR}/bowtie-9999-fix-isa-return-type.patch" )
-# not needed
-# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
-#PATCHES=(
-#	"${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
-#	"${FILESDIR}/${P}-fix-Intel-compilation.patch"
-#	"${FILESDIR}/${P}-unbundle-seqan.patch"
-#)
-# other patches to be still considered
-#	"${FILESDIR}/${P}-fix-setBegin-call.patch"
-#	"${FILESDIR}/${P}-seqan-popcount.patch"
-#	"${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
-#	"${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
-#	"${FILESDIR}/${P}-spelling.patch"
-#	"${FILESDIR}/${P}-tbb-tinythread-missing.patch"
-#)
-
-src_prepare() {
-	default
-
-	# remove bundled libraries, use system seqan 1.4
-	# rm -rf SeqAn-1.1/ third_party/ || die
-
-	# innocuous non-security flags, prevent log pollution
-	append-cxxflags \
-		-Wno-unused-local-typedefs \
-		-Wno-unused-but-set-variable \
-		-Wno-unused-variable
-}
-
-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
-}