| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| update-paths | Updates the main Trinity program to use FHS paths | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| collections15-to-4 | compatibility fix due to use of newer libcommons-collections4-java | Michael R. Crusoe <crusoe@debian.org> | yes | |||
| 0002-fix_istream_failure_call.patch | fix_istream_failure_call Upstream is using wrong test gor file open failure, comparing an int instead of calling fail() method |
Olivier Sallou <osallou@debian.org> | no | 2015-08-20 | ||
| fix_system_paths | drop some use of FindBin and hardcode paths | Tim Booth <tbooth@ceh.ac.uk> | not-needed | |||
| disable-version-check | Disable the version "phone home" for privacy | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| adjust-trimmomatic-adapters-path | Match the Debian's path | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| NeedlemanWunschGotohBanded.patch | using banded DP alignment | Brian Haas <brianjohnhaas@gmail.com> | no | 2016-10-28 | ||
| python3 | Default to running Python 3 | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| unfix_num_of_cores | Don't hardcode number of --CPU (especially above 2) blastn -num_threads will not accept a number larger than the cores/CPUs it detects and will exit with an error. Some Debian test (virtual) machines only have two cores and thus they failed our testing. With this patch we detect in a unix/macOS friendly way the number of cores using `nproc` or `sysctl -n hw.physicalcpu` (respectively). Thus execution of the sample_data tests will be much faster for most developers/users. Perhaps Trinity itself could be taught this trick and the --CPU option would not be needed by default. |
Michael R. Crusoe <crusoe@debian.org> | no | |||
| hardening | add standard CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigsand https://github.com/trinityrnaseq/trinityrnaseq/pull/1090 | Michael R. Crusoe <crusoe@debian.org> | yes | |||
| seqtk-trinity-hardening | Add LDFALGS CPPFLAGS and unshadow CFALGS | Michael R. Crusoe <crusoe@debian.org> | yes | |||
| skip_gatk_test | Skip tests that require GATK4 until it gets packaged | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| skip_tximportData_tests | r-bioc-tximportdata is 400MiB+ package | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| submake | Enable better use of sub-makeand https://github.com/trinityrnaseq/trinity_ext_sample_data/pull/2 and https://github.com/trinityrnaseq/trinityrnaseq/pull/1091 |
Michael R. Crusoe <crusoe@debian.org> | yes | |||
| skip_blat | skip tests with a dependency on blat | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| fix-gcc-10.patch | Fix gcc-10 build issue | Andreas Tille <tille@debian.org> | yes | debian | 2020-08-05 | |
| bamsifter_build | Build bamsifter using the system htslib | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| strip_m64 | remove -m64 flag, hopefully helps arm64 compile | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| extending_Function_in_jung.patch | various fields in libjung-free-java have a type that now extends Function, so that they use apply() instead of transform(). | Pierre Gruet <pgt@debian.org> | not-needed | 2021-11-15 | ||
| R_4.2_fix | Fix heatmap.3.R broken by R 4.2.x+ | Michael R. Crusoe <crusoe@debian.org> | yes |