Moved to tree

Signed-off-by: Justin Lecher <jlec@gentoo.org>

9 files changed, 0 insertions, 338 deletions

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
deleted file mode 100644
index 6530be026..000000000
--- a/sci-biology/bowtie/ChangeLog
+++ /dev/null
@@ -1,37 +0,0 @@
-# ChangeLog for sci-biology/bowtie
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Id$
-
-*bowtie-2.2.6 (10 Oct 2015)
-
-  10 Oct 2015; Ted Tanberry <ted.tanberry@gmail.com> +bowtie-2.2.6.ebuild:
-  sci-biology/bowtie: Version bump to 2.2.6, support dev-cpp/tbb with
-  USE flag.
-
-*bowtie-1.1.2 (10 Oct 2015)
-
-  10 Oct 2015; Ted Tanberry <ted.tanberry@gmail.com> +bowtie-1.1.2.ebuild,
-  +files/bowtie-1.1.2-tbb-tinythread-missing.patch, metadata.xml:
-  sci-biology/bowtie: Version bump to 1.1.2, support dev-cpp/tbb with
-  USE flag.
-
-  08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
-  sci-biology/bowtie: Updating remote-id in metadata.xml
-
-  01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bowtie-1.1.1.ebuild,
-  bowtie-2.2.3.ebuild, bowtie-2.2.5.ebuild:
-  sci-biology/bowtie: clarified package descriptions (bowtie1 vs. bowtie2)
-
-*bowtie-2.2.3 (27 Apr 2015)
-*bowtie-2.2.5 (27 Apr 2015)
-
-  27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  +bowtie-2.2.3.ebuild, +bowtie-2.2.5.ebuild, -bowtie-2.2.4.ebuild:
-  sci-biology/bowtie: version bump
-
-  06 Feb 2015; Ted Tanberry <ted.tanberry@gmail.com> bowtie-1.1.1.ebuild,
-  bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build
-  system bugs
-
-  28 Sep 2013; Justin Lecher <jlec@gentoo.org> bowtie-2.1.0.ebuild:
-  Exchange common variables, fix SRC_URI
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
deleted file mode 100644
index dbc0aab6a..000000000
--- a/sci-biology/bowtie/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST bowtie-1.1.1-src.zip 7711451 SHA256 92aacb2d32065ebee433ce76eff673c24ed12591eb6c20e22ad7e4a790c48f72 SHA512 b7e2604902d846e5e1ce79ae79eceed5401070e7db76f6875d1617e277f8244a32930b334b20869c712bab58d7d88ae26f2569350c8324df4dddae0400c013f9 WHIRLPOOL 65d1248280b32ca1f6cf7c270895abdfbec27f32128915b13a01e43a7697a743f1872440f528b29413140c260e9b7f61b6a4d435f3f83be486972b6b1533d6a5
-DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7
-DIST bowtie2-2.2.3-source.zip 5724584 SHA256 c4f5ce9f0f53a6b8c7f573a26e96f6909f25bd4e0e8bd77191eaa10671baf0bf SHA512 3baf0e764a79e34b6767a62d52777fc528a82481f417ea5f1b24f38e01fac68c2870daff3060c8da11681d3270e15a10ede034356522336a94f0936d70874684 WHIRLPOOL e19ea1cee85c5ccbc198a981587e8832ebfb4bd9a02332d8171d218e89e6c84df5760db6cd1f8195b712097c6ff3ae7790415d1e63afd2632979392709de26ab
-DIST bowtie2-2.2.5-source.zip 5725798 SHA256 e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0 SHA512 8b97860fea73ef36a60dee3dbccdfc956ac7f619ec47a7b820d1df09cff8f77362ddc8071b59ea8021444bda59757d68bdf486fb453d5c4e4b896198bc465d60 WHIRLPOOL 7a8eb7e6d723ccb807a1db3b724326764f8f339017c0b4eb6b234e034458e736ba521106bcc8347c3c428008d8f138f463f3c3e6033b781e1c41898735c2a878
-DIST bowtie2-2.2.6-source.zip 5728779 SHA256 1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f WHIRLPOOL 4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298
diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild
deleted file mode 100644
index 387e06c6e..000000000
--- a/sci-biology/bowtie/bowtie-1.1.1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Short read (below 50nt) aligner requiring end-to-end match, no gaps"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-IUSE="examples"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-src_prepare() {
-	# Suppress useless -Wall pollution
-	sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die
-}
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		CPP="$(tc-getCXX)" \
-		CFLAGS="" \
-		CXXFLAGS="" \
-		EXTRA_FLAGS="${LDFLAGS}" \
-		RELEASE_FLAGS="${CXXFLAGS}"
-}
-
-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-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild
deleted file mode 100644
index 1988f6b18..000000000
--- a/sci-biology/bowtie/bowtie-1.1.2.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Short read (below 50nt) aligner requiring end-to-end match, no gaps"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-IUSE="examples tbb"
-
-DEPEND="app-arch/unzip
-	tbb? ( dev-cpp/tbb )"
-RDEPEND=""
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-src_prepare() {
-	# Suppress useless -Wall pollution
-	sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die
-
-	# always include tinythread.cpp
-	epatch "${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-2.2.3.ebuild b/sci-biology/bowtie/bowtie-2.2.3.ebuild
deleted file mode 100644
index fb766ec6e..000000000
--- a/sci-biology/bowtie/bowtie-2.2.3.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples cpu_flags_x86_sse2"
-REQUIRED_USE="cpu_flags_x86_sse2"
-
-RDEPEND="dev-lang/perl"
-DEPEND="${RDEPEND}
-		app-arch/unzip"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		CPP="$(tc-getCXX)" \
-		CFLAGS="" \
-		CXXFLAGS="" \
-		EXTRA_FLAGS="${LDFLAGS}" \
-		RELEASE_FLAGS="${CXXFLAGS} -msse2"
-}
-
-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
-}
diff --git a/sci-biology/bowtie/bowtie-2.2.5.ebuild b/sci-biology/bowtie/bowtie-2.2.5.ebuild
deleted file mode 100644
index fb766ec6e..000000000
--- a/sci-biology/bowtie/bowtie-2.2.5.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples cpu_flags_x86_sse2"
-REQUIRED_USE="cpu_flags_x86_sse2"
-
-RDEPEND="dev-lang/perl"
-DEPEND="${RDEPEND}
-		app-arch/unzip"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		CPP="$(tc-getCXX)" \
-		CFLAGS="" \
-		CXXFLAGS="" \
-		EXTRA_FLAGS="${LDFLAGS}" \
-		RELEASE_FLAGS="${CXXFLAGS} -msse2"
-}
-
-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
-}
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 fce298569..000000000
--- a/sci-biology/bowtie/bowtie-2.2.6.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples cpu_flags_x86_sse2 tbb"
-REQUIRED_USE="cpu_flags_x86_sse2"
-
-RDEPEND="dev-lang/perl"
-DEPEND="${RDEPEND}
-		app-arch/unzip
-		tbb? ( dev-cpp/tbb )"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		CPP="$(tc-getCXX)" \
-		CFLAGS="" \
-		CXXFLAGS="" \
-		EXTRA_FLAGS="${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
-}
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
deleted file mode 100644
index 2a081ff29..000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- bowtie-1.1.2/Makefile
-+++ bowtie-1.1.2/Makefile
-@@ -106,10 +106,7 @@
- endif
- 
- OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
--             edit.cpp ebwt.cpp
--ifneq (1,$(WITH_TBB))
--	OTHER_CPPS += tinythread.cpp
--endif
-+             edit.cpp ebwt.cpp tinythread.cpp
- 
- SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \
-               log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \
diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
deleted file mode 100644
index 1aef69014..000000000
--- a/sci-biology/bowtie/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-biology</herd>
-  <upstream>
-    <remote-id type="sourceforge">bowtie-bio</remote-id>
-  </upstream>
-  <use>
-    <flag name='tbb'>Enables building bowtie with the Intel 
-      Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This 
-      flag is recommended.</flag>
-  </use>
-</pkgmetadata>