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sci-biology/bowtie: version bump, SLOT major version
sci-biology/bowtie is now SLOTed, in order to allow for a parallel installation with bowtie2. In addition, the latest bowtie now supports dev-cpp/tbb with 'tbb' USE flag.
This commit is contained in:
Ted Tanberry
committed by
Justin Lecher
Justin Lecher
parent
91c97a5dae
commit
ddbfba3594
@@ -1,2 +1,2 @@
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DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800
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DIST bowtie-1.0.0-src.zip 7710572 SHA256 51e434a78e053301f82ae56f4e94f71f97b19f7175324777a7305c8f88c5bac5 SHA512 d867a61c9d4caa2fbe8161b93acc9ccf04294055796a82ccf8d6456019e97299d90d9f16492f873606ae394bbc735108fc97ddf4e5d576a7376f3f9744118831 WHIRLPOOL a70d6516db8ee0c8838795e3b1df0ae1986342cee5dcafd80a39b06cb07ece79d7ebfc6e88b36625d9b33f4f42f559364f42dd4d881fd729c27eac9e673951a1
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DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7
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DIST bowtie2-2.2.6-source.zip 5728779 SHA256 1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f WHIRLPOOL 4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298
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@@ -1,44 +0,0 @@
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# Copyright 1999-2013 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Id$
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EAPI=4
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inherit eutils toolchain-funcs
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DESCRIPTION="An ultrafast memory-efficient short read aligner"
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HOMEPAGE="http://bowtie-bio.sourceforge.net/"
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SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
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LICENSE="Artistic"
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SLOT="0"
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IUSE=""
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KEYWORDS="amd64 x86 ~x64-macos"
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DEPEND="app-arch/unzip"
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RDEPEND=""
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# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
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# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
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src_prepare() {
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epatch "${FILESDIR}"/${P}-gcc-47.patch
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}
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src_compile() {
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unset CFLAGS
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emake \
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CC="$(tc-getCC)" \
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CPP="$(tc-getCXX)" \
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CXX="$(tc-getCXX)" \
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EXTRA_FLAGS="${LDFLAGS}" \
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RELEASE_FLAGS=""
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}
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src_install() {
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dobin bowtie bowtie-*
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exeinto /usr/share/${PN}/scripts
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doexe scripts/*
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newman MANUAL bowtie.1
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dodoc AUTHORS NEWS TUTORIAL
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}
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@@ -1,42 +0,0 @@
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# Copyright 1999-2013 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Id$
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EAPI=5
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inherit eutils toolchain-funcs
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DESCRIPTION="An ultrafast memory-efficient short read aligner"
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HOMEPAGE="http://bowtie-bio.sourceforge.net/"
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SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
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LICENSE="Artistic"
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SLOT="0"
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IUSE=""
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KEYWORDS="~amd64 ~x86 ~x64-macos"
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DEPEND="app-arch/unzip"
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RDEPEND=""
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src_compile() {
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unset CFLAGS
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emake \
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CC="$(tc-getCC)" \
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CPP="$(tc-getCXX)" \
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CXX="$(tc-getCXX)" \
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EXTRA_FLAGS="${LDFLAGS}" \
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RELEASE_FLAGS="${CXXFLAGS}"
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}
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src_install() {
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dobin bowtie bowtie-*
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exeinto /usr/share/${PN}/scripts
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doexe scripts/*
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insinto /usr/share/${PN}
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doins -r genomes indexes
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newman MANUAL bowtie.1
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dodoc AUTHORS NEWS TUTORIAL doc/README
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dohtml doc/{manual.html,style.css}
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}
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58
sci-biology/bowtie/bowtie-1.1.2.ebuild
Normal file
58
sci-biology/bowtie/bowtie-1.1.2.ebuild
Normal file
@@ -0,0 +1,58 @@
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# Copyright 1999-2015 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Id$
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EAPI=5
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inherit eutils toolchain-funcs
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DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
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HOMEPAGE="http://bowtie-bio.sourceforge.net/"
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SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
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LICENSE="Artistic"
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SLOT="1"
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KEYWORDS="~amd64 ~x86 ~x64-macos"
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IUSE="examples tbb"
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DEPEND="app-arch/unzip
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tbb? ( dev-cpp/tbb )"
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RDEPEND=""
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DOCS=( AUTHORS NEWS TUTORIAL doc/README )
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HTML_DOCS=( doc/{manual.html,style.css} )
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src_prepare() {
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# Suppress useless -Wall pollution
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sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die
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# always include tinythread.cpp
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epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
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}
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src_compile() {
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emake \
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CC="$(tc-getCC)" \
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CPP="$(tc-getCXX)" \
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CFLAGS="" \
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CXXFLAGS="" \
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EXTRA_FLAGS="${LDFLAGS}" \
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RELEASE_FLAGS="${CXXFLAGS}" \
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WITH_TBB="$(usex tbb 1 0)"
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}
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src_install() {
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dobin ${PN} ${PN}-*
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exeinto /usr/libexec/${PN}
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doexe scripts/*
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newman MANUAL ${PN}.1
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einstalldocs
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if use examples; then
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insinto /usr/share/${PN}
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doins -r genomes indexes
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fi
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}
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@@ -1,45 +0,0 @@
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alphabet.h | 24 ++++++++++++------------
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1 files changed, 12 insertions(+), 12 deletions(-)
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diff --git a/alphabet.h b/alphabet.h
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index b464ddf..08d0281 100644
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--- a/alphabet.h
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+++ b/alphabet.h
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@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) {
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return s_rc;
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}
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+/// Reverse a string in-place
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+template <typename TStr>
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+static inline void reverseInPlace(TStr& s) {
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+ typedef typename Value<TStr>::Type TVal;
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+ size_t len = length(s);
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+ for(size_t i = 0; i < (len>>1); i++) {
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+ TVal tmp = s[i];
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+ s[i] = s[len-i-1];
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+ s[len-i-1] = tmp;
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+ }
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+}
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+
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/**
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* Reverse-complement s in-place. Ns go to Ns.
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*/
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@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) {
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}
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}
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-/// Reverse a string in-place
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-template <typename TStr>
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-static inline void reverseInPlace(TStr& s) {
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- typedef typename Value<TStr>::Type TVal;
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- size_t len = length(s);
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- for(size_t i = 0; i < (len>>1); i++) {
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- TVal tmp = s[i];
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- s[i] = s[len-i-1];
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- s[len-i-1] = tmp;
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- }
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-}
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-
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/**
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* Return the reverse-complement of s.
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*/
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@@ -0,0 +1,14 @@
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--- bowtie-1.1.2/Makefile
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+++ bowtie-1.1.2/Makefile
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@@ -106,10 +106,7 @@
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endif
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OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
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- edit.cpp ebwt.cpp
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-ifneq (1,$(WITH_TBB))
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- OTHER_CPPS += tinythread.cpp
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-endif
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+ edit.cpp ebwt.cpp tinythread.cpp
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SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \
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log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \
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@@ -5,4 +5,9 @@
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<upstream>
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<remote-id type="sourceforge">bowtie-bio</remote-id>
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</upstream>
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<use>
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<flag name='tbb'>Enables building bowtie with the Intel
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Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This
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flag is recommended.</flag>
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</use>
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</pkgmetadata>
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