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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2019-03-30 00:28:32 +0100 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2019-03-30 00:28:32 +0100 |
| commit | 346ebf0f53a5e272706bcb6ad909ad72a62bb4c7 (patch) | |
| tree | 481ae81b8d6d6bd9bf81339b011ce16d3df8d4f8 /sci-biology/bowtie | |
| parent | sci-biology/repeatmasker: rewamp configuration code (diff) | |
| download | sci-346ebf0f53a5e272706bcb6ad909ad72a62bb4c7.tar.gz sci-346ebf0f53a5e272706bcb6ad909ad72a62bb4c7.tar.bz2 sci-346ebf0f53a5e272706bcb6ad909ad72a62bb4c7.zip | |
sci-biology/bowtie: add another upstream patch
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Diffstat (limited to 'sci-biology/bowtie')
| -rw-r--r-- | sci-biology/bowtie/bowtie-2.3.5-r1.ebuild | 3 | ||||
| -rw-r--r-- | sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch | 15 | ||||
| -rw-r--r-- | sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch | 2 |
3 files changed, 19 insertions, 1 deletions
diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild index f79dcb9cb..2a6fc04eb 100644 --- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild +++ b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild @@ -27,7 +27,8 @@ 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 ) +PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch + "${FILESDIR}"/bowtie-2.3.5-fix-fifo.patch ) pkg_pretend() { if ! use cpu_flags_x86_sse2 ; then 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 new file mode 100644 index 000000000..136bb1e69 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch @@ -0,0 +1,15 @@ +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 index b2f24a7fa..45d6a0f96 100644 --- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch +++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch @@ -1,3 +1,5 @@ +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 |