Debian Patches

Status for trinityrnaseq/2.15.2+dfsg-1

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

All known versions for source package 'trinityrnaseq'

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