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

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

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;
+ 	}