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@fold.natur.cuni.cz>

8 files changed, 236 insertions, 0 deletions

diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
new file mode 100644
index 000000000..58e5c5299
--- /dev/null
+++ b/sci-biology/bowtie/Manifest
@@ -0,0 +1,2 @@
+DIST bowtie-1.2.2-src.zip 7758948 BLAKE2B 76f16f1383af9caf18776616b28556124b02eba39236de745cff902feff85312c98972009a503229658ba4b6b13d6b5470373792de8703d1ef7ffc25ec11f5a7 SHA512 60e44515088c9a67b46b66bcab0c96e25134f5ef6b001f87b1992c6185d6a9e0addb4ddddc65036e1614d697ba9546bca4990bdc8b3a217b0506fafec69c01ce
+DIST bowtie2-2.3.4.3-source.zip 17156180 BLAKE2B 4004aa417f318f5540b129eb97d7f14d31b087c77bb767d547b195d3b966ec272fe7df5888d60b5501330d2ac011f05bdc9b062fa34d5b96b2b29ea0b6167a5c SHA512 9e048c1a86a479c5fe728a492129372d2366d6c50530e05db3faad5ac055596d9f95ac0a9f50099ab3dd945893a587c02e8aaa9b62cc3ead75f6691c52413a2f
diff --git a/sci-biology/bowtie/bowtie-1.2.2.ebuild b/sci-biology/bowtie/bowtie-1.2.2.ebuild
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>