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* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
@ 2013-09-27 15:05 Nicolas Bock
  0 siblings, 0 replies; 6+ messages in thread
From: Nicolas Bock @ 2013-09-27 15:05 UTC (permalink / raw
  To: gentoo-commits

commit:     a504fdf4dfc52876baaa84103a3f6727a3419ec6
Author:     cel <cel.gentoo <AT> gmail <DOT> com>
AuthorDate: Wed Sep 25 21:55:16 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Sep 25 21:55:16 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a504fdf4

sci-biology/bowtie: Added ebuild for bowtie-2.1.0.

---
 sci-biology/bowtie/bowtie-2.1.0.ebuild             | 61 ++++++++++++++++++++++
 .../bowtie/files/bowtie-2.1.0-buildsystem.patch    | 20 +++++++
 sci-biology/bowtie/metadata.xml                    |  5 ++
 3 files changed, 86 insertions(+)

diff --git a/sci-biology/bowtie/bowtie-2.1.0.ebuild b/sci-biology/bowtie/bowtie-2.1.0.ebuild
new file mode 100644
index 0000000..c2c5024
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.1.0.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-source.zip"
+
+LICENSE="GPL-3"
+SLOT="2"
+IUSE="sse2 examples"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="dev-lang/perl"
+DEPEND="${CDEPEND} \
+		app-arch/unzip"
+RDEPEND="${CDEPEND}"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+pkg_pretend() {
+	if ! use sse2 ; then
+		ebegin
+		eerror "bowtie2 requires sse2 support. Please make sure your system supports"
+		eerror "sse2 and enable the sse2 use flag."
+		eend
+		die
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}/${P}-buildsystem.patch"
+}
+
+src_compile() {
+	use sse2 && append-cxxflags -msse2
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+	dobin bowtie2 bowtie2-*
+	exeinto /usr/share/${PN}2/scripts
+	doexe scripts/*
+
+	newman MANUAL bowtie2.1
+	dodoc AUTHORS NEWS TUTORIAL
+	dohtml doc/manual.html doc/style.css
+
+	if use examples; then
+		insinto /usr/share/${PN}2
+		doins -r example
+	fi
+}

diff --git a/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch b/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
new file mode 100644
index 0000000..97300b1
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
@@ -0,0 +1,20 @@
+--- Makefile.old	2013-09-22 12:07:12.606844000 +0200
++++ Makefile	2013-09-22 13:06:03.113888200 +0200
+@@ -24,8 +24,6 @@
+ 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
+@@ -141,7 +139,7 @@
+ 
+ DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
+-RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(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

diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/bowtie/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
@ 2015-02-08 21:07 Christoph Junghans
  0 siblings, 0 replies; 6+ messages in thread
From: Christoph Junghans @ 2015-02-08 21:07 UTC (permalink / raw
  To: gentoo-commits

commit:     59c62dccda24a226ceb535dee59e081c4f1002eb
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Thu Feb  5 21:54:51 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Feb  6 20:24:01 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=59c62dcc

Updated sci-biology/bowtie. Bowtie1 is now properly slotted in SLOT=1. Additional build system fixes.

---
 sci-biology/bowtie/bowtie-1.1.1.ebuild             | 42 ++++++++++++++++++++++
 .../{bowtie-2.1.0.ebuild => bowtie-2.2.4.ebuild}   | 14 ++++----
 .../bowtie/files/bowtie-1.1.1-buildsystem.patch    | 37 +++++++++++++++++++
 ...system.patch => bowtie-2.2.4-buildsystem.patch} | 21 ++++++-----
 4 files changed, 97 insertions(+), 17 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild
new file mode 100644
index 0000000..ad20591
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit base eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/bowtie-1.1.1-src.zip"
+
+LICENSE="Artistic"
+SLOT="1"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
+
+src_compile() {
+	unset CFLAGS
+	emake \
+		CXX="$(tc-getCXX)" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+	dobin bowtie bowtie-*
+	exeinto /usr/share/${PN}/scripts
+	doexe scripts/*
+
+	insinto /usr/share/${PN}
+	doins -r genomes indexes
+
+	newman MANUAL bowtie.1
+	dodoc AUTHORS NEWS TUTORIAL doc/README
+	dohtml doc/{manual.html,style.css}
+}

diff --git a/sci-biology/bowtie/bowtie-2.1.0.ebuild b/sci-biology/bowtie/bowtie-2.2.4.ebuild
similarity index 82%
rename from sci-biology/bowtie/bowtie-2.1.0.ebuild
rename to sci-biology/bowtie/bowtie-2.2.4.ebuild
index aedf017..19e0bca 100644
--- a/sci-biology/bowtie/bowtie-2.1.0.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.4.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
 EAPI=5
 
-inherit eutils toolchain-funcs
+inherit base eutils toolchain-funcs
 
 DESCRIPTION="An ultrafast memory-efficient short read aligner"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+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"
@@ -21,6 +21,8 @@ DEPEND="${RDEPEND}
 
 S="${WORKDIR}/${PN}2-${PV}"
 
+PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
+
 pkg_pretend() {
 	grep "sse2" /proc/cpuinfo > /dev/null
 	if [[ $? -ne 0 ]] ; then
@@ -28,14 +30,10 @@ pkg_pretend() {
 	fi
 }
 
-src_prepare() {
-	epatch "${FILESDIR}/${P}-buildsystem.patch"
-}
-
 src_compile() {
 	emake \
 		CC="$(tc-getCC)" \
-		CPP="$(tc-getCXX)" \
+		CXX="$(tc-getCXX)" \
 		EXTRA_FLAGS="${LDFLAGS}" \
 		RELEASE_FLAGS="${CXXFLAGS} -msse2"
 }

diff --git a/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch b/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch
new file mode 100644
index 0000000..9563a33
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch
@@ -0,0 +1,37 @@
+--- 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-2.1.0-buildsystem.patch b/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch
similarity index 55%
rename from sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
rename to sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch
index 97300b1..8b9218b 100644
--- a/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
+++ b/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch
@@ -1,19 +1,22 @@
---- Makefile.old	2013-09-22 12:07:12.606844000 +0200
-+++ Makefile	2013-09-22 13:06:03.113888200 +0200
-@@ -24,8 +24,6 @@
+--- Makefile
++++ Makefile
+@@ -22,11 +22,6 @@
+ #
+ 
  INC =
- GCC_PREFIX = $(shell dirname `which gcc`)
- GCC_SUFFIX =
+-GCC_PREFIX = $(shell dirname `which gcc`)
+-GCC_SUFFIX =
 -CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
 -CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
- CXX = $(CPP)
+-CXX = $(CPP)
  HEADERS = $(wildcard *.h)
  BOWTIE_MM = 1
-@@ -141,7 +139,7 @@
+ BOWTIE_SHARED_MEM = 0
+@@ -152,7 +147,7 @@
  
- DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
  DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
--RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
+-RELEASE_FLAGS  = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
 +RELEASE_FLAGS  = $(CXXFLAGS)
  RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
  NOASSERT_FLAGS = -DNDEBUG


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
@ 2015-10-12  6:51 Marius Brehler
  0 siblings, 0 replies; 6+ messages in thread
From: Marius Brehler @ 2015-10-12  6:51 UTC (permalink / raw
  To: gentoo-commits

commit:     72ec06023243088ee31dacc6a9189c986c011561
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sat Oct 10 17:21:59 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sat Oct 10 17:21:59 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=72ec0602

sci-biology/bowtie: Version bump to 1.1.2

dev-cpp/tbb is now supported with 'tbb' USE flag.

 sci-biology/bowtie/ChangeLog                       |  7 +++
 sci-biology/bowtie/bowtie-1.1.2.ebuild             | 64 ++++++++++++++++++++++
 .../bowtie-1.1.2-tbb-tinythread-missing.patch      | 14 +++++
 sci-biology/bowtie/metadata.xml                    |  5 ++
 4 files changed, 90 insertions(+)

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index e05b4dc..42bdbdf 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+*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
 

diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild
new file mode 100644
index 0000000..e443686
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild
@@ -0,0 +1,64 @@
+# 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}/${P}-tbb-tinythread-missing.patch"
+}
+
+src_compile() {
+	if use tbb ; then
+		TBB="1"
+	else
+		TBB="0"
+	fi
+
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CFLAGS="" \
+		CXXFLAGS="" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS}" \
+		WITH_TBB="${TBB}"
+}
+
+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-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
new file mode 100644
index 0000000..2a081ff
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch
@@ -0,0 +1,14 @@
+--- 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
index e493417..1aef690 100644
--- a/sci-biology/bowtie/metadata.xml
+++ b/sci-biology/bowtie/metadata.xml
@@ -5,4 +5,9 @@
   <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] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
@ 2019-02-18 13:44 Martin Mokrejs
  0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2019-02-18 13:44 UTC (permalink / raw
  To: gentoo-commits

commit:     3c65e999c45f956a48f434581ed74f27732c9c2a
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb 18 13:44:27 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb 18 13:44:27 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3c65e999

sci-biology/bowtie: add some compile patches from Debian

Seems both bowtie1 and bowtie2 are bound too much to SeqAn-1.1
and need more patches for SeqAn-1.4. Per reports on github
it seems one should be able to compile bowtie-1.2.2 using
-std=c++03 (but not me).

Package-Manager: Portage-2.3.59, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/bowtie/bowtie-1.2.2.ebuild             | 77 ++++++++++++++++++++++
 sci-biology/bowtie/bowtie-2.3.4.3.ebuild           | 62 +++++++++++++++++
 .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch   | 17 +++++
 .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 +++++++++
 .../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 +++++
 7 files changed, 234 insertions(+)

diff --git a/sci-biology/bowtie/bowtie-1.2.2.ebuild b/sci-biology/bowtie/bowtie-1.2.2.ebuild
new file mode 100644
index 000000000..cae085bff
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.2.2.ebuild
@@ -0,0 +1,77 @@
+# 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
+}

diff --git a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild b/sci-biology/bowtie/bowtie-2.3.4.3.ebuild
new file mode 100644
index 000000000..eea3059cf
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.3.4.3.ebuild
@@ -0,0 +1,62 @@
+# 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-${PV}-source.zip"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS=""
+
+IUSE="examples cpu_flags_x86_sse2 +tbb"
+
+RDEPEND="dev-lang/perl
+	tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	sys-libs/readline"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+DOCS=( AUTHORS NEWS TUTORIAL )
+HTML_DOCS=( doc/{manual.html,style.css} )
+#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update
+
+pkg_pretend() {
+	if ! use cpu_flags_x86_sse2 ; then
+		eerror "This package requires a CPU supporting the SSE2 instruction set."
+		die "SSE2 support missing"
+	fi
+}
+
+src_compile() {
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CXX="$(tc-getCXX)" \
+		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-1.2.2-_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-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

diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
new file mode 100644
index 000000000..71e8d3bb8
--- /dev/null
+++ b/sci-biology/bowtie/metadata.xml
@@ -0,0 +1,16 @@
+<?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] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
@ 2019-02-19 11:21 Martin Mokrejs
  0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2019-02-19 11:21 UTC (permalink / raw
  To: gentoo-commits

commit:     85794dc2e25580c628e007d4a528ffc2e24d4239
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 19 11:20:51 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 19 11:20:51 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=85794dc2

sci-biology/bowtie: working 1.2.2 snapshot

This ebuild keeps the bundled SeqAn-1.1 sources (a library of
headers) and does not insist on system-wide installed
SeqAn-1.4 (for which too many patches are needed and I am unable
to evaluate/apply them all).

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

 .../bowtie/bowtie-1.2.2_beta20190219.ebuild        | 81 ++++++++++++++++++++++
 sci-biology/bowtie/bowtie-9999.ebuild              | 81 ++++++++++++++++++++++
 .../files/bowtie-1.2.2-fix-isa-return-type.patch   | 22 ++++++
 3 files changed, 184 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..fcf0b4516
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
@@ -0,0 +1,81 @@
+# 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"
+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-9999.ebuild b/sci-biology/bowtie/bowtie-9999.ebuild
new file mode 100644
index 000000000..d54d0a544
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-9999.ebuild
@@ -0,0 +1,81 @@
+# 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
+}

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; }


^ permalink raw reply related	[flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
@ 2019-03-27 22:46 Martin Mokrejs
  0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2019-03-27 22:46 UTC (permalink / raw
  To: gentoo-commits

commit:     2b44f30b60c65d2485250cb71e7dabe10a2694a6
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 27 22:45:47 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 27 22:45:47 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2b44f30b

sci-biology/bowtie: patch --interleaved, add KEYWORDS

Do not unset contents of CFLAGS and CXXFLAGS.
Thanks to ch4rr0 at
https://github.com/BenLangmead/bowtie2/issues/239

Add deemed patch from
https://github.com/BenLangmead/bowtie2/issues/240

Added KEYWORDS.

Closes: https://bugs.gentoo.org/649824
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 .../bowtie/{bowtie-2.3.5.ebuild => bowtie-2.3.5-r1.ebuild}  |  5 ++---
 sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch | 13 +++++++++++++
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-2.3.5.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
similarity index 94%
rename from sci-biology/bowtie/bowtie-2.3.5.ebuild
rename to sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
index dd4d8be66..f79dcb9cb 100644
--- a/sci-biology/bowtie/bowtie-2.3.5.ebuild
+++ b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
@@ -12,7 +12,7 @@ SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-$
 
 LICENSE="GPL-3"
 SLOT="2"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 
 IUSE="examples cpu_flags_x86_sse2 +tbb"
 
@@ -27,6 +27,7 @@ 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 )
 
 pkg_pretend() {
 	if ! use cpu_flags_x86_sse2 ; then
@@ -40,8 +41,6 @@ src_compile() {
 		CC="$(tc-getCC)" \
 		CPP="$(tc-getCXX)" \
 		CXX="$(tc-getCXX)" \
-		CFLAGS="" \
-		CXXFLAGS="" \
 		EXTRA_FLAGS="${LDFLAGS}" \
 		RELEASE_FLAGS="${CXXFLAGS} -msse2" \
 		WITH_TBB="$(usex tbb 1 0)"

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
new file mode 100644
index 000000000..b2f24a7fa
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
@@ -0,0 +1,13 @@
+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] 6+ messages in thread
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2019-03-27 22:46 Martin Mokrejs
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