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commit: 346ebf0f53a5e272706bcb6ad909ad72a62bb4c7 |
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Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Fri Mar 29 23:28:32 2019 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Fri Mar 29 23:28:32 2019 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=346ebf0f |
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|
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sci-biology/bowtie: add another upstream patch |
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|
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Package-Manager: Portage-2.3.62, Repoman-2.3.12 |
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Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> |
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|
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sci-biology/bowtie/bowtie-2.3.5-r1.ebuild | 3 ++- |
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sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch | 15 +++++++++++++++ |
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.../bowtie/files/bowtie-2.3.5-fix-interleaved.patch | 2 ++ |
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3 files changed, 19 insertions(+), 1 deletion(-) |
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|
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diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild |
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index f79dcb9cb..2a6fc04eb 100644 |
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--- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild |
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+++ b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild |
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@@ -27,7 +27,8 @@ S="${WORKDIR}/${PN}2-${PV}" |
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DOCS=( AUTHORS NEWS TUTORIAL ) |
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HTML_DOCS=( doc/{manual.html,style.css} ) |
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#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update |
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-PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch ) |
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+PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch |
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+ "${FILESDIR}"/bowtie-2.3.5-fix-fifo.patch ) |
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|
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pkg_pretend() { |
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if ! use cpu_flags_x86_sse2 ; then |
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|
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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 |
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new file mode 100644 |
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index 000000000..136bb1e69 |
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--- /dev/null |
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+++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch |
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@@ -0,0 +1,15 @@ |
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+https://github.com/BenLangmead/bowtie2/commit/d7eab7cf6b7e238047044cf61acc662b05c772c4 |
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+ |
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+diff --git a/pat.cpp b/pat.cpp |
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+index 453ba69..6d862f8 100644 |
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+--- a/pat.cpp |
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++++ b/pat.cpp |
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+@@ -494,7 +494,7 @@ void CFilePatternSource::open() { |
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+ |
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+ is_fifo = S_ISFIFO(st.st_mode) != 0; |
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+ #endif |
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+- if (pp_.format != BAM || is_fifo || is_gzipped_file(fd)) { |
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++ if (pp_.format != BAM && (is_fifo || is_gzipped_file(fd))) { |
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+ zfp_ = gzdopen(fd, "r"); |
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+ compressed_ = true; |
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+ } else { |
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|
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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 |
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index b2f24a7fa..45d6a0f96 100644 |
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--- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch |
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+++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch |
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@@ -1,3 +1,5 @@ |
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+https://github.com/BenLangmead/bowtie2/commit/753df9deca210db54e1ecc94f946b413876e456e |
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+ |
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diff --git bowtie-2.3.5/bt2_search.cpp b/bt2_search.cpp |
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index 1d53741..c59e39c 100644 |
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--- bowtie-2.3.5/bt2_search.cpp |
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