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

[Martin Mokrejs]

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;
- 	}