[med-svn] [Git][med-team/transdecoder][master] 12 commits: New upstream version

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / transdecoder


Commits:
d7514718 by Michael R. Crusoe at 2026-05-01T13:11:51+02:00
New upstream version

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ba94bab7 by Michael R. Crusoe at 2026-05-01T13:11:52+02:00
New upstream version 6.0.0
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56b78753 by Michael R. Crusoe at 2026-05-01T13:12:08+02:00
Update upstream source from tag 'upstream/6.0.0'

Update to upstream version '6.0.0'
with Debian dir a0015ad9ff2deb2726a415273737dd76cb565322
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697416b8 by Michael R. Crusoe at 2026-05-01T13:12:08+02:00
Standards-Version: 4.7.4 (routine-update)

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54e70f03 by Michael R. Crusoe at 2026-05-01T13:14:03+02:00
debputy lint --auto-fix (routine-update)

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92b1345f by Michael R. Crusoe at 2026-05-01T13:16:17+02:00
Removed 2 patches applied upstream.

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e463afb9 by Michael R. Crusoe at 2026-05-01T12:16:37+01:00
Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

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2f56034c by Michael R. Crusoe at 2026-05-01T14:23:01+02:00
d/{tests/,}control: new dependency: diamond-aligner

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ff037043 by Michael R. Crusoe at 2026-05-01T18:16:30+02:00
d/rules: more comprehensively remove errant execute bits.

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5d0edb39 by Michael R. Crusoe at 2026-05-01T18:16:30+02:00
d/tests/control: remove skip-not-installable and make explicit where we test (limited by hmmer): arm64, amd64, & i386.

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d877b672 by Michael R. Crusoe at 2026-05-01T18:16:30+02:00
Create manual pages.

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5fe35233 by Michael R. Crusoe at 2026-05-01T18:17:01+02:00
release to unstable

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36 changed files:

- Changelog.txt
- Docker/Dockerfile
- Docker/VERSION.txt
- Docker/make_simg.sh
- PerlLib/DelimParser.pm
- PerlLib/GFF3_utils2.pm
- PerlLib/GTF.pm
- PerlLib/GTF_utils2.pm
- PerlLib/PWM.pm
- PerlLib/Pipeliner.pm
- README.md
- + TransDecoder
- debian/changelog
- debian/control
- − debian/createmanpages
- − debian/patches/2to3.patch
- debian/patches/series
- − debian/patches/test_path.patch
- debian/rules
- debian/tests/control
- debian/transdecoder.links
- + debian/transdecoder.manpages
- debian/upstream/metadata
- sample_data/cufflinks_example/runMe.sh
- sample_data/pasa_example/runMe.sh
- sample_data/simple_transcriptome_target/runMe.Docker.sh
- sample_data/simple_transcriptome_target/runMe.sh
- sample_data/stringtie_example/runMe.sh
- sample_data/supertranscripts_example/runMe.sh
- TransDecoder.LongOrfs → util/TransDecoder.LongOrfs
- TransDecoder.Predict → util/TransDecoder.Predict
- util/gff3_file_to_bed.pl
- util/gtf_genome_to_cdna_fasta.pl
- util/misc/get_FP_FN_scores.py
- util/misc/plot_indiv_seq_likelihood_profile.py
- util/misc/select_TD_orfs.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/transdecoder/-/compare/e2fc450c1def6ca8450b083fc50c71ba713740f3...5fe35233d5b1c09880d1cc457f1b061b7b1765c6

-- 
View it on GitLab: https://salsa.debian.org/med-team/transdecoder/-/compare/e2fc450c1def6ca8450b083fc50c71ba713740f3...5fe35233d5b1c09880d1cc457f1b061b7b1765c6
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