Michael R. Crusoe pushed to branch master at Debian Med / bowtie2
Commits:
7bfaa165 by Michael R. Crusoe at 2019-12-15T09:18:30Z
set M64_FLAG and POPCNT_CAPABILITY; 64bit archs only
- - - - -
42ade843 by Michael R. Crusoe at 2019-12-15T15:16:27Z
fix building in with cowdancer or eatmydata
- - - - -
2b056b8c by Michael R. Crusoe at 2019-12-15T15:16:27Z
add missing ${perl:Depends}
- - - - -
1cb4b2ab by Michael R. Crusoe at 2019-12-15T15:16:28Z
build everywhere again
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -2,6 +2,10 @@ bowtie2 (2.3.5.1-3) unstable; urgency=medium
* Team upload.
* Enable all architectures via simde.
+ * Unset M64_FLAG and POPCNT_CAPABILITY on non AMD64 archs.
+ * debian/rules: Fix testing in with cowdancer or eatmydata by unsetting
+ LD_PRELOAD (the address sanitizer must be first in the library list)
+ * Added missing ${perl:Depends} for the bowtie2 binary package
-- Michael R. Crusoe <[email protected]> Sat, 14 Dec 2019 13:42:14
+0100
=====================================
debian/control
=====================================
@@ -23,7 +23,8 @@ Package: bowtie2
Architecture: any
Depends: python3,
${misc:Depends},
- ${shlibs:Depends}
+ ${shlibs:Depends},
+ ${perl:Depends}
Suggests: bowtie2-examples
Description: ultrafast memory-efficient short read aligner
is an ultrafast and memory-efficient tool for aligning sequencing reads
=====================================
debian/rules
=====================================
@@ -13,8 +13,11 @@ export DEB_CXXFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3
EXTRA_OPTIONS =
ifneq ($(DEB_HOST_ARCH),amd64)
- EXTRA_OPTIONS = NO_TBB=1
+ EXTRA_OPTIONS += NO_TBB=1 POPCNT_CAPABILITY= M64_FLAG=
+else
+ EXTRA_OPTIONS += POPCNT_CAPABILITY=1 M64_FLAG=-m64
endif
+
export EXTRA_OPTIONS
%:
@@ -36,7 +39,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
bowtie2-align-l-sanitized \
bowtie2-build-s-sanitized \
bowtie2-build-l-sanitized
- make -j1 test
+ env --unset=LD_PRELOAD make -j1 test
endif
override_dh_auto_install:
@@ -47,15 +50,15 @@ override_dh_install:
override_dh_installman:
mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
- debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*"
- debian/help2man-wrapper $(pkg)-build "wrapper for $(pkg)-build-*"
- debian/help2man-wrapper $(pkg)-build-l "building a colorspace index for
$(pkg)"
- debian/help2man-wrapper $(pkg)-build-s "building a colorspace index for
$(pkg)"
- debian/help2man-wrapper $(pkg)-inspect "wrapper for $(pkg)-inspect-*
index"
- debian/help2man-wrapper $(pkg)-inspect-l "extracts information from a
$(pkg) index"
- debian/help2man-wrapper $(pkg)-inspect-s "extracts information from a
$(pkg) index"
- debian/help2man-wrapper $(pkg)-align-l "ultrafast and memory-efficient
backend tool for aligning sequencing reads to long reference sequences"
- debian/help2man-wrapper $(pkg)-align-s "ultrafast and memory-efficient
backend tool for aligning sequencing reads to long reference sequences"
+ env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg) "wrapper for
$(pkg)-align-*"
+ env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-build "wrapper
for $(pkg)-build-*"
+ env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-build-l "building
a colorspace index for $(pkg)"
+ env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-build-s "building
a colorspace index for $(pkg)"
+ env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-inspect "wrapper
for $(pkg)-inspect-* index"
+ env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-inspect-l
"extracts information from a $(pkg) index"
+ env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-inspect-s
"extracts information from a $(pkg) index"
+ env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-align-l
"ultrafast and memory-efficient backend tool for aligning sequencing reads to
long reference sequences"
+ env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-align-s
"ultrafast and memory-efficient backend tool for aligning sequencing reads to
long reference sequences"
rm -f $(CURDIR)/debian/$(pkg)/usr/bin/bowtie2-buildc
override_dh_installchangelogs:
View it on GitLab:
https://salsa.debian.org/med-team/bowtie2/compare/d06dfdbed5448bd1387ca58dafdd88c50cd1431a...1cb4b2ab49f3a058f0de9240f448fa42fb33c72e
--
View it on GitLab:
https://salsa.debian.org/med-team/bowtie2/compare/d06dfdbed5448bd1387ca58dafdd88c50cd1431a...1cb4b2ab49f3a058f0de9240f448fa42fb33c72e
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