From b6846dd42e04e42c0103983272b6db0db248f75a Mon Sep 17 00:00:00 2001
From: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Tue, 19 Feb 2019 12:26:14 +0100
Subject: sci-biology/bowtie: removing not working -1.2.2 ebuild

Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
---
 sci-biology/bowtie/Manifest            |  1 -
 sci-biology/bowtie/bowtie-1.2.2.ebuild | 77 ----------------------------------
 2 files changed, 78 deletions(-)
 delete mode 100644 sci-biology/bowtie/bowtie-1.2.2.ebuild

(limited to 'sci-biology/bowtie')

diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 58e5c5299..87beeab0c 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,2 +1 @@
-DIST bowtie-1.2.2-src.zip 7758948 BLAKE2B 76f16f1383af9caf18776616b28556124b02eba39236de745cff902feff85312c98972009a503229658ba4b6b13d6b5470373792de8703d1ef7ffc25ec11f5a7 SHA512 60e44515088c9a67b46b66bcab0c96e25134f5ef6b001f87b1992c6185d6a9e0addb4ddddc65036e1614d697ba9546bca4990bdc8b3a217b0506fafec69c01ce
 DIST bowtie2-2.3.4.3-source.zip 17156180 BLAKE2B 4004aa417f318f5540b129eb97d7f14d31b087c77bb767d547b195d3b966ec272fe7df5888d60b5501330d2ac011f05bdc9b062fa34d5b96b2b29ea0b6167a5c SHA512 9e048c1a86a479c5fe728a492129372d2366d6c50530e05db3faad5ac055596d9f95ac0a9f50099ab3dd945893a587c02e8aaa9b62cc3ead75f6691c52413a2f
diff --git a/sci-biology/bowtie/bowtie-1.2.2.ebuild b/sci-biology/bowtie/bowtie-1.2.2.ebuild
deleted file mode 100644
index cae085bff..000000000
--- a/sci-biology/bowtie/bowtie-1.2.2.ebuild
+++ /dev/null
@@ -1,77 +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
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS=""
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	sci-biology/seqan:1.4
-	app-arch/unzip"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-PATCHES=(
-	"${FILESDIR}/${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
-}
-- 
cgit v1.2.3-65-gdbad