| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| use_bwa_compatible_fermi-lite.patch | Adapt to fermi-lite which does not conflict with bwa An issue on fermi-lite upstream tracker https://github.com/lh3/fermi-lite/issues/5 suggests to take over a patch for the Debian package which would enable making it co-usable with libbwa-dev (which is needed in libseqlib). This patch adapts ariba to the potential change in fermi-lite. |
Andreas Tille <tille@debian.org> | no | 2017-02-04 | ||
| add-testdata.patch | include testdata in package | Sascha Steinbiss <satta@debian.org> | no | 2019-09-09 | ||
| use_debian_packaged_libs_for_extension.patch | use Debian packages dependencies for extension build | Sascha Steinbiss <satta@debian.org> | no | |||
| disable-tests-with-internet-access.patch | disable tests that need Internet access | Sascha Steinbiss <satta@debian.org> | no | 2019-09-09 | ||
| support-pymummer-0.11.patch | adapt test cases for new PyMUMmer version pymummer 0.11 uses a different internal format which is incompatible with the one assumed by Ariba. Note that ariba hard-requires an earlier version than the one in Debian. However, since Debian has updated pymummer now, we need to catch up even though upstream does not. |
Sascha Steinbiss <satta@debian.org> | no | 2020-06-30 | ||
| run-debian-spades-wrapper.patch | run Debian SPAdes wrapper Debian's /usr/bin/spades.py is not a Python script, but a wrapper around a common executable only provided for compatibility reasons. Ariba is trying to execute it explicitly as a Python script. This patch just calls the executable without forcing it through the Python interpreter. |
Sascha Steinbiss <satta@debian.org> | no | 2020-06-30 | ||
| port-to-pytest.patch | Switch from nose -> pytest as the former is deprecated | Nilesh Patra <nilesh@debian.org> | yes | 2021-12-19 | ||
| mpileup-1.16.patch | move to bcftools 1.16 mpileup The original mpileup command from samtools has been deprecated and removed starting with version 1.16. The command has been moved to bcftools 1.16. This patch adjusts the pysam call to reach for bcftools appropriately instead of the plain samtools wrapper. |
Étienne Mollier <emollier@debian.org> | yes | debian upstream | 2022-11-28 | |
| skip-cluster-test.patch | skip tests using dataset from older samtools mpileup This will need to be reverted once new upstream versions support htslib / samtools / bcftools 1.16. |
Étienne Mollier <emollier@debian.org> | not-needed | debian upstream | 2022-11-28 | |
| adjust-bowtie2-test.patch | skip tests failing with new bowtie2 Some of the test data seem to need | Étienne Mollier <emollier@debian.org> | yes | debian upstream | 2022-12-14 |