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

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* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
@ 2021-03-06 10:02 Andrew Ammerlaan
  0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 10:02 UTC (permalink / raw
  To: gentoo-commits

commit:     718c86792641e4203877c23d69e9d4dcb0274388
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 10:02:43 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 10:02:43 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=718c8679

sci-biology/bowtie: drop old

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../bowtie/bowtie-1.2.2_beta20190219.ebuild        | 81 ----------------------
 .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch   | 17 -----
 .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 ---------
 .../files/bowtie-1.2.2-fix-isa-return-type.patch   | 22 ------
 .../bowtie/files/bowtie-1.2.2-unbundle-seqan.patch | 14 ----
 .../bowtie/files/bowtie-1.2.2-void2int.patch       | 16 -----
 6 files changed, 182 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
deleted file mode 100644
index f7a1b92d4..000000000
--- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2020 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"
-COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-#	sci-biology/seqan:1.4"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" )
-# not needed
-# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
-#
-# still to be considered
-#PATCHES=(
-#	"${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
-#	"${FILESDIR}/${P}-unbundle-seqan.patch"
-#	"${FILESDIR}/${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 library of headers, 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
-}

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch
deleted file mode 100644
index 4bcd61ba3..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Description: Change class name of _Context_LSS
- New version 1.4 of SeQan uses a different name of the class. 
-Forwarded: no
-Author: Gert Wollny <gw.fossdev@gmail.com>
-Last-Update: 2014-100-06
-
---- bowtie-1.2.2/diff_sample.h	2017-11-03 01:25:56.000000000 +0100
-+++ bowtie-1.2.2/diff_sample.h	2019-02-18 12:50:37.894674282 +0100
-@@ -979,7 +979,7 @@
- 	{
- 		Timer timer(cout, "  Invoking Larsson-Sadakane on ranks time: ", this->verbose());
- 		VMSG_NL("  Invoking Larsson-Sadakane on ranks");
--		_Context_LSS<TIndexOff> c;
-+		ContextLss_<TIndexOff> c;
- 		c.suffixsort(
- 			(TIndexOff*)begin(_isaPrime, Standard()),
- 			(TIndexOff*)begin(sPrime, Standard()),

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch
deleted file mode 100644
index 75942efb5..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-fix compilation errors with Intel compilers:
-error: no operator "=" matches these operands
-author: Ward Poelmans
---- bowtie-1.2.2/hit.h	2018-01-24 12:57:47.135575442 +0100
-+++ bowtie-1.2.2/hit.h	2018-01-24 12:57:58.615869774 +0100
-@@ -640,10 +640,26 @@
- 			s.moveTo(btString);
- 		}
- 
-+		batch(const batch &other)
-+                {
-+                    batchId = other.batchId;
-+                    isWritten = other.isWritten;
-+                    btString = other.btString;
-+                }
-+
- 		bool operator<(const batch& other) const {
- 			return batchId < other.batchId;
- 		}
- 
-+		batch& operator=(batch&& other) {
-+			if (&other != this) {
-+				batchId = other.batchId;
-+				isWritten = other.isWritten;
-+				other.btString.moveTo(btString);
-+			}
-+			return *this;
-+		}
-+
- 		batch& operator=(batch& other) {
- 			if (&other != this) {
- 				batchId = other.batchId;

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
deleted file mode 100644
index de19e42a8..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From 58c6ac97b1938909881877ef83167f5eff0e8ab1 Mon Sep 17 00:00:00 2001
-From: Rone Charles <rone_charles@fastmail.com>
-Date: Tue, 4 Sep 2018 21:06:39 -0400
-Subject: [PATCH] Fix isa return type
-
----
- ebwt.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/ebwt.h b/ebwt.h
-index fe6300cc..8f886b8d 100644
---- a/ebwt.h
-+++ b/ebwt.h
-@@ -862,7 +862,7 @@ class Ebwt {
- 	TIndexOffU*   ftab() const         { return _ftab; }
- 	TIndexOffU*   eftab() const        { return _eftab; }
- 	TIndexOffU*   offs() const         { return _offs; }
--	uint32_t*   isa() const          { return _isa; } /* check */
-+	TIndexOffU*   isa() const          { return _isa; } /* check */
- 	TIndexOffU*   plen() const         { return _plen; }
- 	TIndexOffU*   rstarts() const      { return _rstarts; }
- 	uint8_t*    ebwt() const         { return _ebwt; }

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch
deleted file mode 100644
index b1a5f98f5..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- bowtie-1.2.2/Makefile	2019-02-18 13:26:29.490835084 +0100
-+++ bowtie-1.2.2/Makefile	2019-02-18 13:28:36.864742545 +0100
-@@ -5,10 +5,7 @@
- prefix = /usr/local
- bindir = $(prefix)/bin
- 
--SEQAN_DIR = ./SeqAn-1.1
--# treat SeqAn as a sysdir to suppress warnings
--SEQAN_INC = -isystem $(SEQAN_DIR)
--INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
-+INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) `pkg-config --cflags seqan-1.4` -I third_party
- CPP = g++
- CXX = $(CPP)
- CC = gcc

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch b/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch
deleted file mode 100644
index 822b673ae..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-#The latest Intel compiler (2016,2017) complains about the incompatibility of "void *" argument
-#being incompatible with parameter of type "int *"
-#M. Fujinaga (fujinaga@ualberta.ca)
---- processor_support.h	2017-02-02 21:48:42.436432756 +0000
-+++ processor_support.h	2017-02-02 21:48:54.419309743 +0000
-@@ -44,8 +44,8 @@
- 
-     try {
- #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) )
--        __cpuid((void *) &regs,0); // test if __cpuid() works, if not catch the exception
--        __cpuid((void *) &regs,0x1); // POPCNT bit is bit 23 in ECX
-+        __cpuid((int *) &regs,0); // test if __cpuid() works, if not catch the exception
-+        __cpuid((int *) &regs,0x1); // POPCNT bit is bit 23 in ECX
- #elif defined(USING_GCC_COMPILER)
-         __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
- #else


^ permalink raw reply related	[flat|nested] 7+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
@ 2021-12-13 12:28 Andrew Ammerlaan
  0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-12-13 12:28 UTC (permalink / raw
  To: gentoo-commits

commit:     d635c86902bb7d00ae05c542f2ec3be0a32a76cd
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 13 12:26:55 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Dec 13 12:26:55 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d635c869

sci-biology/bowtie: remove duplicate

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 .../bowtie/bowtie-1.2.2_beta20190219.ebuild        | 81 ----------------------
 sci-biology/bowtie/bowtie-1.3.0.ebuild             | 63 -----------------
 sci-biology/bowtie/bowtie-2.4.2.ebuild             | 62 -----------------
 .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch   | 17 -----
 .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 ---------
 .../files/bowtie-1.2.2-fix-isa-return-type.patch   | 22 ------
 .../bowtie/files/bowtie-1.2.2-unbundle-seqan.patch | 14 ----
 .../bowtie/files/bowtie-1.2.2-void2int.patch       | 16 -----
 sci-biology/bowtie/metadata.xml                    | 16 -----
 9 files changed, 323 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
deleted file mode 100644
index 857bc9cd1..000000000
--- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-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"
-COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-#	sci-biology/seqan:1.4"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-#PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" )
-# not needed
-# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
-#
-# still to be considered
-#PATCHES=(
-#	"${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
-#	"${FILESDIR}/${P}-unbundle-seqan.patch"
-#	"${FILESDIR}/${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 library of headers, 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
-}

diff --git a/sci-biology/bowtie/bowtie-1.3.0.ebuild b/sci-biology/bowtie/bowtie-1.3.0.ebuild
deleted file mode 100644
index 118cc1303..000000000
--- a/sci-biology/bowtie/bowtie-1.3.0.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="https://github.com/BenLangmead/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-#	sci-biology/seqan:1.4"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-src_prepare() {
-	default
-
-	# remove bundled library of headers, 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
-}

diff --git a/sci-biology/bowtie/bowtie-2.4.2.ebuild b/sci-biology/bowtie/bowtie-2.4.2.ebuild
deleted file mode 100644
index 03cf3f8a9..000000000
--- a/sci-biology/bowtie/bowtie-2.4.2.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="https://github.com/BenLangmead/${PN}2/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples cpu_flags_x86_sse2 +tbb" # sra
-# IUSE=sra Use sra-toolkit to download input datasets on the fly.
-
-RDEPEND="dev-lang/perl
-	tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	sys-libs/readline"
-#	sra? ( sci-biology/sra_sdk )"
-
-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)" \
-		EXTRA_FLAGS="${LDFLAGS}" \
-		RELEASE_FLAGS="${CXXFLAGS} -msse2" \
-		WITH_TBB="$(usex tbb 1 0)"
-		# USE_SRA="$(usex sra 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-1.2.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch
deleted file mode 100644
index 4bcd61ba3..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Description: Change class name of _Context_LSS
- New version 1.4 of SeQan uses a different name of the class. 
-Forwarded: no
-Author: Gert Wollny <gw.fossdev@gmail.com>
-Last-Update: 2014-100-06
-
---- bowtie-1.2.2/diff_sample.h	2017-11-03 01:25:56.000000000 +0100
-+++ bowtie-1.2.2/diff_sample.h	2019-02-18 12:50:37.894674282 +0100
-@@ -979,7 +979,7 @@
- 	{
- 		Timer timer(cout, "  Invoking Larsson-Sadakane on ranks time: ", this->verbose());
- 		VMSG_NL("  Invoking Larsson-Sadakane on ranks");
--		_Context_LSS<TIndexOff> c;
-+		ContextLss_<TIndexOff> c;
- 		c.suffixsort(
- 			(TIndexOff*)begin(_isaPrime, Standard()),
- 			(TIndexOff*)begin(sPrime, Standard()),

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch
deleted file mode 100644
index 75942efb5..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-fix compilation errors with Intel compilers:
-error: no operator "=" matches these operands
-author: Ward Poelmans
---- bowtie-1.2.2/hit.h	2018-01-24 12:57:47.135575442 +0100
-+++ bowtie-1.2.2/hit.h	2018-01-24 12:57:58.615869774 +0100
-@@ -640,10 +640,26 @@
- 			s.moveTo(btString);
- 		}
- 
-+		batch(const batch &other)
-+                {
-+                    batchId = other.batchId;
-+                    isWritten = other.isWritten;
-+                    btString = other.btString;
-+                }
-+
- 		bool operator<(const batch& other) const {
- 			return batchId < other.batchId;
- 		}
- 
-+		batch& operator=(batch&& other) {
-+			if (&other != this) {
-+				batchId = other.batchId;
-+				isWritten = other.isWritten;
-+				other.btString.moveTo(btString);
-+			}
-+			return *this;
-+		}
-+
- 		batch& operator=(batch& other) {
- 			if (&other != this) {
- 				batchId = other.batchId;

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
deleted file mode 100644
index de19e42a8..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From 58c6ac97b1938909881877ef83167f5eff0e8ab1 Mon Sep 17 00:00:00 2001
-From: Rone Charles <rone_charles@fastmail.com>
-Date: Tue, 4 Sep 2018 21:06:39 -0400
-Subject: [PATCH] Fix isa return type
-
----
- ebwt.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/ebwt.h b/ebwt.h
-index fe6300cc..8f886b8d 100644
---- a/ebwt.h
-+++ b/ebwt.h
-@@ -862,7 +862,7 @@ class Ebwt {
- 	TIndexOffU*   ftab() const         { return _ftab; }
- 	TIndexOffU*   eftab() const        { return _eftab; }
- 	TIndexOffU*   offs() const         { return _offs; }
--	uint32_t*   isa() const          { return _isa; } /* check */
-+	TIndexOffU*   isa() const          { return _isa; } /* check */
- 	TIndexOffU*   plen() const         { return _plen; }
- 	TIndexOffU*   rstarts() const      { return _rstarts; }
- 	uint8_t*    ebwt() const         { return _ebwt; }

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch
deleted file mode 100644
index b1a5f98f5..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- bowtie-1.2.2/Makefile	2019-02-18 13:26:29.490835084 +0100
-+++ bowtie-1.2.2/Makefile	2019-02-18 13:28:36.864742545 +0100
-@@ -5,10 +5,7 @@
- prefix = /usr/local
- bindir = $(prefix)/bin
- 
--SEQAN_DIR = ./SeqAn-1.1
--# treat SeqAn as a sysdir to suppress warnings
--SEQAN_INC = -isystem $(SEQAN_DIR)
--INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
-+INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) `pkg-config --cflags seqan-1.4` -I third_party
- CPP = g++
- CXX = $(CPP)
- CC = gcc

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch b/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch
deleted file mode 100644
index 822b673ae..000000000
--- a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-#The latest Intel compiler (2016,2017) complains about the incompatibility of "void *" argument
-#being incompatible with parameter of type "int *"
-#M. Fujinaga (fujinaga@ualberta.ca)
---- processor_support.h	2017-02-02 21:48:42.436432756 +0000
-+++ processor_support.h	2017-02-02 21:48:54.419309743 +0000
-@@ -44,8 +44,8 @@
- 
-     try {
- #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) )
--        __cpuid((void *) &regs,0); // test if __cpuid() works, if not catch the exception
--        __cpuid((void *) &regs,0x1); // POPCNT bit is bit 23 in ECX
-+        __cpuid((int *) &regs,0); // test if __cpuid() works, if not catch the exception
-+        __cpuid((int *) &regs,0x1); // POPCNT bit is bit 23 in ECX
- #elif defined(USING_GCC_COMPILER)
-         __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
- #else

diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
deleted file mode 100644
index 71e8d3bb8..000000000
--- a/sci-biology/bowtie/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <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>


^ permalink raw reply related	[flat|nested] 7+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
@ 2021-03-16 18:15 Andrew Ammerlaan
  0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-03-16 18:15 UTC (permalink / raw
  To: gentoo-commits

commit:     841b73539cdc92799497752d37b764c16793582b
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Mar 16 18:11:02 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Mar 16 18:11:02 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=841b7353

Revert "sci-biology/bowtie: drop old"

This reverts commit 718c86792641e4203877c23d69e9d4dcb0274388.

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../bowtie/bowtie-1.2.2_beta20190219.ebuild        | 81 ++++++++++++++++++++++
 .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch   | 17 +++++
 .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 +++++++++
 .../files/bowtie-1.2.2-fix-isa-return-type.patch   | 22 ++++++
 .../bowtie/files/bowtie-1.2.2-unbundle-seqan.patch | 14 ++++
 .../bowtie/files/bowtie-1.2.2-void2int.patch       | 16 +++++
 6 files changed, 182 insertions(+)

diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
new file mode 100644
index 000000000..f7a1b92d4
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2020 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"
+COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660"
+
+LICENSE="Artistic"
+SLOT="1"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="examples +tbb"
+
+RDEPEND="tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+#	sci-biology/seqan:1.4"
+
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" )
+# not needed
+# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
+#
+# still to be considered
+#PATCHES=(
+#	"${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
+#	"${FILESDIR}/${P}-unbundle-seqan.patch"
+#	"${FILESDIR}/${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 library of headers, 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
+}

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch
new file mode 100644
index 000000000..4bcd61ba3
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch
@@ -0,0 +1,17 @@
+Description: Change class name of _Context_LSS
+ New version 1.4 of SeQan uses a different name of the class. 
+Forwarded: no
+Author: Gert Wollny <gw.fossdev@gmail.com>
+Last-Update: 2014-100-06
+
+--- bowtie-1.2.2/diff_sample.h	2017-11-03 01:25:56.000000000 +0100
++++ bowtie-1.2.2/diff_sample.h	2019-02-18 12:50:37.894674282 +0100
+@@ -979,7 +979,7 @@
+ 	{
+ 		Timer timer(cout, "  Invoking Larsson-Sadakane on ranks time: ", this->verbose());
+ 		VMSG_NL("  Invoking Larsson-Sadakane on ranks");
+-		_Context_LSS<TIndexOff> c;
++		ContextLss_<TIndexOff> c;
+ 		c.suffixsort(
+ 			(TIndexOff*)begin(_isaPrime, Standard()),
+ 			(TIndexOff*)begin(sPrime, Standard()),

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch
new file mode 100644
index 000000000..75942efb5
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch
@@ -0,0 +1,32 @@
+fix compilation errors with Intel compilers:
+error: no operator "=" matches these operands
+author: Ward Poelmans
+--- bowtie-1.2.2/hit.h	2018-01-24 12:57:47.135575442 +0100
++++ bowtie-1.2.2/hit.h	2018-01-24 12:57:58.615869774 +0100
+@@ -640,10 +640,26 @@
+ 			s.moveTo(btString);
+ 		}
+ 
++		batch(const batch &other)
++                {
++                    batchId = other.batchId;
++                    isWritten = other.isWritten;
++                    btString = other.btString;
++                }
++
+ 		bool operator<(const batch& other) const {
+ 			return batchId < other.batchId;
+ 		}
+ 
++		batch& operator=(batch&& other) {
++			if (&other != this) {
++				batchId = other.batchId;
++				isWritten = other.isWritten;
++				other.btString.moveTo(btString);
++			}
++			return *this;
++		}
++
+ 		batch& operator=(batch& other) {
+ 			if (&other != this) {
+ 				batchId = other.batchId;

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
new file mode 100644
index 000000000..de19e42a8
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
@@ -0,0 +1,22 @@
+From 58c6ac97b1938909881877ef83167f5eff0e8ab1 Mon Sep 17 00:00:00 2001
+From: Rone Charles <rone_charles@fastmail.com>
+Date: Tue, 4 Sep 2018 21:06:39 -0400
+Subject: [PATCH] Fix isa return type
+
+---
+ ebwt.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/ebwt.h b/ebwt.h
+index fe6300cc..8f886b8d 100644
+--- a/ebwt.h
++++ b/ebwt.h
+@@ -862,7 +862,7 @@ class Ebwt {
+ 	TIndexOffU*   ftab() const         { return _ftab; }
+ 	TIndexOffU*   eftab() const        { return _eftab; }
+ 	TIndexOffU*   offs() const         { return _offs; }
+-	uint32_t*   isa() const          { return _isa; } /* check */
++	TIndexOffU*   isa() const          { return _isa; } /* check */
+ 	TIndexOffU*   plen() const         { return _plen; }
+ 	TIndexOffU*   rstarts() const      { return _rstarts; }
+ 	uint8_t*    ebwt() const         { return _ebwt; }

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch
new file mode 100644
index 000000000..b1a5f98f5
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch
@@ -0,0 +1,14 @@
+--- bowtie-1.2.2/Makefile	2019-02-18 13:26:29.490835084 +0100
++++ bowtie-1.2.2/Makefile	2019-02-18 13:28:36.864742545 +0100
+@@ -5,10 +5,7 @@
+ prefix = /usr/local
+ bindir = $(prefix)/bin
+ 
+-SEQAN_DIR = ./SeqAn-1.1
+-# treat SeqAn as a sysdir to suppress warnings
+-SEQAN_INC = -isystem $(SEQAN_DIR)
+-INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
++INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) `pkg-config --cflags seqan-1.4` -I third_party
+ CPP = g++
+ CXX = $(CPP)
+ CC = gcc

diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch b/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch
new file mode 100644
index 000000000..822b673ae
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch
@@ -0,0 +1,16 @@
+#The latest Intel compiler (2016,2017) complains about the incompatibility of "void *" argument
+#being incompatible with parameter of type "int *"
+#M. Fujinaga (fujinaga@ualberta.ca)
+--- processor_support.h	2017-02-02 21:48:42.436432756 +0000
++++ processor_support.h	2017-02-02 21:48:54.419309743 +0000
+@@ -44,8 +44,8 @@
+ 
+     try {
+ #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) )
+-        __cpuid((void *) &regs,0); // test if __cpuid() works, if not catch the exception
+-        __cpuid((void *) &regs,0x1); // POPCNT bit is bit 23 in ECX
++        __cpuid((int *) &regs,0); // test if __cpuid() works, if not catch the exception
++        __cpuid((int *) &regs,0x1); // POPCNT bit is bit 23 in ECX
+ #elif defined(USING_GCC_COMPILER)
+         __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
+ #else


^ permalink raw reply related	[flat|nested] 7+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
@ 2019-12-23 15:38 Martin Mokrejs
  0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2019-12-23 15:38 UTC (permalink / raw
  To: gentoo-commits

commit:     37d6c90ece12854ac4ae220e0d95bc88ec3af1b9
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Dec 23 15:38:01 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Dec 23 15:38:01 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=37d6c90e

sci-biology/bowtie: version bump

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/bowtie/bowtie-2.3.5.1.ebuild           | 60 ++++++++++++++++++++++
 .../bowtie/files/bowtie-2.3.5-fix-fifo.patch       | 15 ------
 .../files/bowtie-2.3.5-fix-interleaved.patch       | 15 ------
 3 files changed, 60 insertions(+), 30 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild b/sci-biology/bowtie/bowtie-2.3.5.1.ebuild
new file mode 100644
index 000000000..c2fef8667
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.3.5.1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit 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-${PV}-source.zip"
+SRC_URI="https://github.com/BenLangmead/${PN}2/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="examples cpu_flags_x86_sse2 +tbb"
+
+RDEPEND="dev-lang/perl
+	tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	sys-libs/readline"
+
+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)" \
+		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-2.3.5-fix-fifo.patch b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch
deleted file mode 100644
index 136bb1e69..000000000
--- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-https://github.com/BenLangmead/bowtie2/commit/d7eab7cf6b7e238047044cf61acc662b05c772c4
-
-diff --git a/pat.cpp b/pat.cpp
-index 453ba69..6d862f8 100644
---- a/pat.cpp
-+++ b/pat.cpp
-@@ -494,7 +494,7 @@ void CFilePatternSource::open() {
- 
- 			is_fifo = S_ISFIFO(st.st_mode) != 0;
- #endif
--			if (pp_.format != BAM || is_fifo || is_gzipped_file(fd)) {
-+			if (pp_.format != BAM && (is_fifo || is_gzipped_file(fd))) {
- 				zfp_ = gzdopen(fd, "r");
- 				compressed_ = true;
- 			} else {

diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
deleted file mode 100644
index 45d6a0f96..000000000
--- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-https://github.com/BenLangmead/bowtie2/commit/753df9deca210db54e1ecc94f946b413876e456e
-
-diff --git bowtie-2.3.5/bt2_search.cpp b/bt2_search.cpp
-index 1d53741..c59e39c 100644
---- bowtie-2.3.5/bt2_search.cpp
-+++ bowtie-2.3.5/bt2_search.cpp
-@@ -1673,7 +1673,7 @@ static void parseOptions(int argc, const char **argv) {
- 		     << "sequences must be specified with -1 and -2." << endl;
- 		throw 1;
- 	}
--	if(interleaved && (format != FASTA || format != FASTQ)) {
-+	if(interleaved && (format != FASTA && format != FASTQ)) {
- 		cerr << "Error: --interleaved only works in combination with FASTA (-f) and FASTQ (-q) formats." << endl;
- 		throw 1;
- 	}


^ permalink raw reply related	[flat|nested] 7+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
@ 2019-03-29 23:28 Martin Mokrejs
  0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2019-03-29 23:28 UTC (permalink / raw
  To: gentoo-commits

commit:     346ebf0f53a5e272706bcb6ad909ad72a62bb4c7
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 29 23:28:32 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 29 23:28:32 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=346ebf0f

sci-biology/bowtie: add another upstream patch

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/bowtie/bowtie-2.3.5-r1.ebuild                 |  3 ++-
 sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch      | 15 +++++++++++++++
 .../bowtie/files/bowtie-2.3.5-fix-interleaved.patch       |  2 ++
 3 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
index f79dcb9cb..2a6fc04eb 100644
--- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
@@ -27,7 +27,8 @@ S="${WORKDIR}/${PN}2-${PV}"
 DOCS=( AUTHORS NEWS TUTORIAL )
 HTML_DOCS=( doc/{manual.html,style.css} )
 #PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update
-PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch )
+PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch
+	"${FILESDIR}"/bowtie-2.3.5-fix-fifo.patch )
 
 pkg_pretend() {
 	if ! use cpu_flags_x86_sse2 ; then

diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch
new file mode 100644
index 000000000..136bb1e69
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch
@@ -0,0 +1,15 @@
+https://github.com/BenLangmead/bowtie2/commit/d7eab7cf6b7e238047044cf61acc662b05c772c4
+
+diff --git a/pat.cpp b/pat.cpp
+index 453ba69..6d862f8 100644
+--- a/pat.cpp
++++ b/pat.cpp
+@@ -494,7 +494,7 @@ void CFilePatternSource::open() {
+ 
+ 			is_fifo = S_ISFIFO(st.st_mode) != 0;
+ #endif
+-			if (pp_.format != BAM || is_fifo || is_gzipped_file(fd)) {
++			if (pp_.format != BAM && (is_fifo || is_gzipped_file(fd))) {
+ 				zfp_ = gzdopen(fd, "r");
+ 				compressed_ = true;
+ 			} else {

diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
index b2f24a7fa..45d6a0f96 100644
--- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
+++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
@@ -1,3 +1,5 @@
+https://github.com/BenLangmead/bowtie2/commit/753df9deca210db54e1ecc94f946b413876e456e
+
 diff --git bowtie-2.3.5/bt2_search.cpp b/bt2_search.cpp
 index 1d53741..c59e39c 100644
 --- bowtie-2.3.5/bt2_search.cpp


^ permalink raw reply related	[flat|nested] 7+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
@ 2015-10-15 17:12 Justin Lecher
  0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2015-10-15 17:12 UTC (permalink / raw
  To: gentoo-commits

commit:     525b717f7cebfc901579e10b1c45622bddf68eb6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Oct 15 17:12:19 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Oct 15 17:12:19 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=525b717f

Moved to tree

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

 sci-biology/bowtie/ChangeLog                       | 37 --------------
 sci-biology/bowtie/bowtie-1.1.1.ebuild             | 53 --------------------
 sci-biology/bowtie/bowtie-1.1.2.ebuild             | 58 ----------------------
 sci-biology/bowtie/bowtie-2.2.3.ebuild             | 52 -------------------
 sci-biology/bowtie/bowtie-2.2.5.ebuild             | 52 -------------------
 sci-biology/bowtie/bowtie-2.2.6.ebuild             | 54 --------------------
 .../bowtie-1.1.2-tbb-tinythread-missing.patch      | 14 ------
 sci-biology/bowtie/metadata.xml                    | 13 -----
 8 files changed, 333 deletions(-)

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
deleted file mode 100644
index 6530be0..0000000
--- 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/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild
deleted file mode 100644
index 387e06c..0000000
--- 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 1988f6b..0000000
--- 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 fb766ec..0000000
--- 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 fb766ec..0000000
--- 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 fce2985..0000000
--- 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 2a081ff..0000000
--- 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 1aef690..0000000
--- 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>


^ permalink raw reply related	[flat|nested] 7+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
@ 2015-02-08 21:07 Christoph Junghans
  0 siblings, 0 replies; 7+ messages in thread
From: Christoph Junghans @ 2015-02-08 21:07 UTC (permalink / raw
  To: gentoo-commits

commit:     9944df7ebb74c77f354dba013b5ac9d4bdab0c8f
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Fri Feb  6 21:15:40 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Feb  6 21:15:40 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9944df7e

Removed all patches, setting CXXFLAGS and such via emake now. Fixed the wrong manpage categories.

---
 sci-biology/bowtie/ChangeLog                       |  6 +++-
 sci-biology/bowtie/bowtie-1.1.1.ebuild             | 18 ++++++-----
 sci-biology/bowtie/bowtie-2.2.4.ebuild             | 19 +++++------
 .../bowtie/files/bowtie-1.1.1-buildsystem.patch    | 37 ----------------------
 .../bowtie/files/bowtie-2.2.4-buildsystem.patch    | 23 --------------
 5 files changed, 23 insertions(+), 80 deletions(-)

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index 1a636c5..f3d98e2 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/bowtie
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  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/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild
index f152518..bc6d514 100644
--- a/sci-biology/bowtie/bowtie-1.1.1.ebuild
+++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild
@@ -19,16 +19,20 @@ IUSE="examples"
 DEPEND="app-arch/unzip"
 RDEPEND=""
 
-PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
 
 src_prepare() {
-	epatch ${PATCHES[@]}
+	# Suppress useless -Wall pollution
+	sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile
 }
 
 src_compile() {
-	unset CFLAGS
 	emake \
-		CXX="$(tc-getCXX)" \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CFLAGS="" \
+		CXXFLAGS="" \
 		EXTRA_FLAGS="${LDFLAGS}" \
 		RELEASE_FLAGS="${CXXFLAGS}"
 }
@@ -39,10 +43,8 @@ src_install() {
 	exeinto /usr/libexec/${PN}
 	doexe scripts/*
 
-	newman MANUAL ${PN}
-	dodoc AUTHORS NEWS TUTORIAL doc/README
-	docinto html
-	dodoc doc/{manual.html,style.css}
+	newman MANUAL ${PN}.1
+	einstalldocs
 
 	if use examples; then
 		insinto /usr/share/${PN}

diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.4.ebuild
index 4b518ca..d8059fc 100644
--- a/sci-biology/bowtie/bowtie-2.2.4.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.4.ebuild
@@ -23,16 +23,15 @@ DEPEND="${RDEPEND}
 
 S="${WORKDIR}/${PN}2-${PV}"
 
-PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
-
-src_prepare() {
-	epatch ${PATCHES[@]}
-}
+DOCS=( AUTHORS NEWS TUTORIAL )
+HTML_DOCS=( doc/{manual.html,style.css} )
 
 src_compile() {
-	unset CFLAGS
 	emake \
-		CXX="$(tc-getCXX)" \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CFLAGS="" \
+		CXXFLAGS="" \
 		EXTRA_FLAGS="${LDFLAGS}" \
 		RELEASE_FLAGS="${CXXFLAGS} -msse2"
 }
@@ -43,10 +42,8 @@ src_install() {
 	exeinto /usr/libexec/${PN}2
 	doexe scripts/*
 
-	newman MANUAL ${PN}2.2
-	dodoc AUTHORS NEWS TUTORIAL
-	docinto html
-	dodoc doc/{manual.html,style.css}
+	newman MANUAL ${PN}2.1
+	einstalldocs
 
 	if use examples; then
 		insinto /usr/share/${PN}2

diff --git a/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch b/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch
deleted file mode 100644
index 9563a33..0000000
--- a/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- Makefile
-+++ Makefile
-@@ -5,16 +5,11 @@
- SEQAN_DIR = SeqAn-1.1
- SEQAN_INC = -I $(SEQAN_DIR)
- INC = $(SEQAN_INC) -I third_party
--CPP = g++
--CXX = $(CPP)
--CC = gcc
- HEADERS = $(wildcard *.h)
- BOWTIE_MM = 1
- BOWTIE_SHARED_MEM = 1
- EXTRA_FLAGS =
--EXTRA_CFLAGS =
- EXTRA_CXXFLAGS =
--CFLAGS += $(EXTRA_CFLAGS)
- CXXFLAGS += $(EXTRA_CXXFLAGS)
- 
- # Detect Cygwin or MinGW
-@@ -127,7 +122,7 @@
- endif
- 
- DEBUG_FLAGS = -O0 -g3 -m64
--RELEASE_FLAGS = -O3 -m64
-+RELEASE_FLAGS = $(CXXFLAGS)
- NOASSERT_FLAGS = -DNDEBUG
- FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
- 
-@@ -198,7 +193,7 @@
-      $(MM_DEF) \
-      $(SHMEM_DEF)
- 
--ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
-+ALL_FLAGS = $(EXTRA_FLAGS) $(CXXFLAGS)
- DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
- RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
- 

diff --git a/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch b/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch
deleted file mode 100644
index 8b9218b..0000000
--- a/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch
+++ /dev/null
@@ -1,23 +0,0 @@
---- Makefile
-+++ Makefile
-@@ -22,11 +22,6 @@
- #
- 
- INC =
--GCC_PREFIX = $(shell dirname `which gcc`)
--GCC_SUFFIX =
--CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
--CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
--CXX = $(CPP)
- HEADERS = $(wildcard *.h)
- BOWTIE_MM = 1
- BOWTIE_SHARED_MEM = 0
-@@ -152,7 +147,7 @@
- 
- DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
- DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
--RELEASE_FLAGS  = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
-+RELEASE_FLAGS  = $(CXXFLAGS)
- RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
- NOASSERT_FLAGS = -DNDEBUG
- FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE


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2021-03-06 10:02 [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/ Andrew Ammerlaan
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2021-12-13 12:28 Andrew Ammerlaan
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2015-10-15 17:12 Justin Lecher
2015-02-08 21:07 Christoph Junghans

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