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<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Michael R. Crusoe pushed to branch master at <a href="https://salsa.debian.org/med-team/transdecoder">Debian Med / transdecoder</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/d7514718c69f2653a0fa90c00a12514878647e82">d7514718</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T13:11:51+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/ba94bab7b31dbe667d9d0b6400e08475b50f444e">ba94bab7</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T13:11:52+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 6.0.0</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/56b787539371bdeb2e55ace4d99bb4b414b440ca">56b78753</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T13:12:08+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/6.0.0'
Update to upstream version '6.0.0'
with Debian dir a0015ad9ff2deb2726a415273737dd76cb565322</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/697416b8ac70b42fa996eb6dc14a7eb63f39c776">697416b8</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T13:12:08+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.7.4 (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/54e70f038222e9df66a1ec05fa3e013097f12015">54e70f03</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T13:14:03+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>debputy lint --auto-fix (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/92b1345f95333e68b89ac12aba2982e37101a99f">92b1345f</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T13:16:17+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Removed 2 patches applied upstream.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/e463afb91f11bd412fc3f4eba63200cc9c258afc">e463afb9</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T12:16:37+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>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
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/2f56034c9e7f34bb26dd25cc688602c78a15f81c">2f56034c</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T14:23:01+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/{tests/,}control: new dependency: diamond-aligner
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/ff037043d1c55e01b332bb633ee56a91c246fc27">ff037043</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T18:16:30+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: more comprehensively remove errant execute bits.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/5d0edb39c9652a1f83eddc06fc2b90c8ec4f4a8d">5d0edb39</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T18:16:30+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/tests/control: remove skip-not-installable and make explicit where we test (limited by hmmer): arm64, amd64, & i386.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/d877b672466a1272b550ae376b605117e5d31bf3">d877b672</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T18:16:30+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Create manual pages.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/transdecoder/-/commit/5fe35233d5b1c09880d1cc457f1b061b7b1765c6">5fe35233</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-05-01T18:17:01+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>release to unstable
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
36 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#36238d5fa26683466193f61b8d724919bec12681">
Changelog.txt
</a>
</li>
<li class="file-stats">
<a href="#56cd058343dc500d70fb6c2c4aac98dc5da7cbe5">
Docker/Dockerfile
</a>
</li>
<li class="file-stats">
<a href="#bbb101bc2f90c8750e858f6e53300be082686b61">
Docker/VERSION.txt
</a>
</li>
<li class="file-stats">
<a href="#adac835863f7418a1ebc830e14b7c5802897a7c7">
Docker/make_simg.sh
</a>
</li>
<li class="file-stats">
<a href="#95dd0ddbb75226db6d1bdbe34c535a1409b2cc0b">
PerlLib/DelimParser.pm
</a>
</li>
<li class="file-stats">
<a href="#f32b57e13548b81b8dd814b0f27e7acf2208917e">
PerlLib/GFF3_utils2.pm
</a>
</li>
<li class="file-stats">
<a href="#4c5baf9a37211afeaa42c45a8576ab956f496542">
PerlLib/GTF.pm
</a>
</li>
<li class="file-stats">
<a href="#c63eb922fe5c6d3b69848d0ca963838a284d487e">
PerlLib/GTF_utils2.pm
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</li>
<li class="file-stats">
<a href="#654b57fbd284c718ac161e2437c8d79272cfd7c8">
PerlLib/PWM.pm
</a>
</li>
<li class="file-stats">
<a href="#ef90f142804aedff7246e07cab5d18b0eb62a5a7">
PerlLib/Pipeliner.pm
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9895535cf9cfb1f8753d2966dab8cb7437e9a19c">
<span class="new-file">
+
TransDecoder
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="deleted-file">
−
debian/createmanpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="deleted-file">
−
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#2d9bd9e9a028bca2d16643e441a645c01419ddf4">
<span class="deleted-file">
−
debian/patches/test_path.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
</li>
<li class="file-stats">
<a href="#6418ea0eb6040283c0686411c720c8112221e8c1">
debian/transdecoder.links
</a>
</li>
<li class="file-stats">
<a href="#953e9b99e1fec426255b3cf9b9afae7733f327f7">
<span class="new-file">
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debian/transdecoder.manpages
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</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<li class="file-stats">
<a href="#b4e319015d113593f59639d8cdc71d346b6aad05">
sample_data/cufflinks_example/runMe.sh
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<li class="file-stats">
<a href="#43ebbeb05838bfa815f826ebd3531fee7894b4fa">
sample_data/pasa_example/runMe.sh
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<li class="file-stats">
<a href="#c94b549dc9a7804c25a3fe2e9cdcee439b4d3f25">
sample_data/simple_transcriptome_target/runMe.Docker.sh
</a>
</li>
<li class="file-stats">
<a href="#b81194b82457d10eca34560a9c9772715e8cf5a6">
sample_data/simple_transcriptome_target/runMe.sh
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</li>
<li class="file-stats">
<a href="#22785356b75d84d6d6303e2da815b401a4933935">
sample_data/stringtie_example/runMe.sh
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</li>
<li class="file-stats">
<a href="#04c2135054f1ab24a82b88479fe98af3c4f7e5cc">
sample_data/supertranscripts_example/runMe.sh
</a>
</li>
<li class="file-stats">
<a href="#5a2a44eb44e4b203e8103cdb198b57934dc4c735">
TransDecoder.LongOrfs
→
util/TransDecoder.LongOrfs
</a>
</li>
<li class="file-stats">
<a href="#8ce74351356c090db178f9966f0b8d044e631ca7">
TransDecoder.Predict
→
util/TransDecoder.Predict
</a>
</li>
<li class="file-stats">
<a href="#b5fc2e155755843cd09af307d0a89c73ca9c98a0">
util/gff3_file_to_bed.pl
</a>
</li>
<li class="file-stats">
<a href="#9c08e6744eb266cb2cc1a1952ca0ce4b7781ea85">
util/gtf_genome_to_cdna_fasta.pl
</a>
</li>
<li class="file-stats">
<a href="#8682bbc621b3f151a1b34a9ebb51a66dba18b706">
util/misc/get_FP_FN_scores.py
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</li>
<li class="file-stats">
<a href="#c3ff6d6500f5e35cbc85cdf091cbd1ca2854b871">
util/misc/plot_indiv_seq_likelihood_profile.py
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</li>
<li class="file-stats">
<a href="#685a9f9d056184906dc5569bae1103f49667e315">
util/misc/select_TD_orfs.py
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
</h5>
</div>
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