commit: 346ebf0f53a5e272706bcb6ad909ad72a62bb4c7
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 29 23:28:32 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 29 23:28:32 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=346ebf0f
sci-biology/bowtie: add another upstream patch
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/bowtie/bowtie-2.3.5-r1.ebuild | 3 ++-
sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch | 15 +++++++++++++++
.../bowtie/files/bowtie-2.3.5-fix-interleaved.patch | 2 ++
3 files changed, 19 insertions(+), 1 deletion(-)
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
