Package: bowtie2 / 2.3.5.1-1

Metadata

Package Version Patches format
bowtie2 2.3.5.1-1 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
drop not needed js from manual.patch | (download)

doc/manual.html | 3 0 + 3 - 0 !
1 file changed, 3 deletions(-)

 remove link to external js lib, not needed as used for ie browsers
wrong interpreter path.patch | (download)

bowtie2 | 2 1 + 1 - 0 !
bowtie2-build | 2 1 + 1 - 0 !
bowtie2-inspect | 2 1 + 1 - 0 !
3 files changed, 3 insertions(+), 3 deletions(-)

 use path to interpreter instead of /usr/bin/env
hardening.patch | (download)

Makefile | 4 3 + 1 - 0 !
1 file changed, 3 insertions(+), 1 deletion(-)

 patch injects hardening c(pp,xx) flags and ldflags
reproducible.patch | (download)

Makefile | 2 1 + 1 - 0 !
bt2_build.cpp | 18 9 + 9 - 0 !
bt2_inspect.cpp | 18 9 + 9 - 0 !
bt2_search.cpp | 18 9 + 9 - 0 !
4 files changed, 28 insertions(+), 28 deletions(-)

 make build reproducible
 This patch removes the embedding of build specific values like
 hostname, time, etc. from the binary. It also ensures a stable
 sorting order for all wildcard expansions in the Makefile.
skip_test_requiring_non free_libmath random perl.patch | (download)

Makefile | 9 4 + 5 - 0 !
example/reads/simulate.pl | 115 0 + 115 - 0 !
2 files changed, 4 insertions(+), 120 deletions(-)

 math::random is in package libmath-random-perl which is
 unfortunately in non-free thus we can not use it for testing while building
 this package.  Thus the occurrences of references and the surrounding code
 is removed here.

do not rebuild during test.patch | (download)

scripts/sim/run.sh | 18 9 + 9 - 0 !
scripts/test/simple_tests.sh | 24 12 + 12 - 0 !
2 files changed, 21 insertions(+), 21 deletions(-)

 do not rebuild with default settings during test
 The test suite builds the debug versions of the executables with default
 flags, while is needs to be built with the flags in d/rules.
2to3.patch | (download)

Makefile | 4 2 + 2 - 0 !
bowtie2-build | 2 1 + 1 - 0 !
bowtie2-inspect | 2 1 + 1 - 0 !
scripts/sa.py | 8 4 + 4 - 0 !
scripts/test/README.md | 4 2 + 2 - 0 !
scripts/test/benchmark/benchmarks.py | 6 3 + 3 - 0 !
scripts/test/benchmark/run.py | 2 1 + 1 - 0 !
scripts/test/benchmark/samreader.py | 6 3 + 3 - 0 !
scripts/test/bt2face.py | 2 1 + 1 - 0 !
scripts/test/btdata.py | 10 5 + 5 - 0 !
scripts/test/dataface.py | 2 1 + 1 - 0 !
scripts/test/large_idx.py | 6 3 + 3 - 0 !
scripts/test/regressions.py | 2 1 + 1 - 0 !
13 files changed, 28 insertions(+), 28 deletions(-)

 use 2to3 to port to python3
Bug-Debian: https://bugs.debian.org/936233