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; + }
