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Pull requests: bgruening/galaxytools

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Pull requests list

Fix RAG Retriever crash on markdown files
#1859 opened May 4, 2026 by arash77 Contributor Loading…
3 of 5 tasks
Fix RAG embedding download: use snapshot_download instead of SentenceTransformer.save() skip-version-check
#1858 opened May 4, 2026 by arash77 Contributor Loading…
1 task done
2
Updating tools/rna_tools/sortmerna from version 4.4.0 to 5.0.0
#1857 opened May 4, 2026 by gxydevbot Contributor Loading…
Fix no_interp parameter in Cellpose-SAM wrapper
#1853 opened Apr 28, 2026 by kostrykin Collaborator Loading…
3 of 5 tasks
3
[WIP] update ViennaRNA
#1851 opened Apr 26, 2026 by bgruening Owner Loading…
5 tasks
3
Fix Tiara wrapper when outputs are missing
#1846 opened Apr 21, 2026 by Minamehr Contributor Loading…
3 of 5 tasks
10
Image Magick conversion: fix missing font error for svg conversion
#1834 opened Apr 8, 2026 by Delphine-L Contributor Loading…
5 tasks
2
Update 3Dtrees: Detailview to v1.1.1
#1831 opened Apr 7, 2026 by kgerb Collaborator Loading…
3 of 5 tasks
5
Update wget in get_pdb to 1.25.0
#1822 opened Mar 23, 2026 by RZ9082 Collaborator Loading…
2 of 5 tasks
8
Make genome size mandatory in its branch
#1815 opened Mar 18, 2026 by wm75 Collaborator Loading…
5 tasks
3
Updating tools/cellprofiler_v4 from version 4.2.8 to 4.2.8.1
#1812 opened Mar 16, 2026 by gxydevbot Contributor Loading…
Updating tools/cellpose_v4 from version 4.0.8 to 4.1.1
#1795 opened Mar 9, 2026 by gxydevbot Contributor Loading…
2
add WebAtlas pipeline 0.5.3
#1794 opened Mar 3, 2026 by dannyspadaro Loading…
1 of 5 tasks
141
Updating tools/trim_galore from version 0.6.10 to 0.6.11
#1793 opened Mar 2, 2026 by gxydevbot Contributor Loading…
Add WhisperX model download script and configuration files for version 3.4.2
#1792 opened Feb 27, 2026 by arash77 Contributor • Draft
3 of 5 tasks
3
Fix kmetashot tool data table linting
#1787 opened Feb 24, 2026 by paulzierep Contributor Loading…
2
Updating tools/markitdown from version 0.1.4 to 0.1.5
#1784 opened Feb 23, 2026 by gxydevbot Contributor Loading…
update whisperx to 3.8.1
#1776 opened Feb 14, 2026 by bgruening Owner Loading…
11
Updating tools/wordcloud from version 1.9.4 to 1.9.6
#1762 opened Jan 26, 2026 by gxydevbot Contributor Loading…
Improved DM
#1751 opened Jan 13, 2026 by paulzierep Contributor Loading…
Handle RateLimitError in LLM Hub tool
#1743 opened Jan 7, 2026 by arash77 Contributor Loading…
3
Add Cleaverna tool
#1739 opened Dec 26, 2025 by reyhaneh-tavakoli Contributor • Draft
42
Add BioStudies upload tool
#1716 opened Nov 6, 2025 by davelopez Contributor Loading…
2
Feat: Add two additional cellprofiler modules
#1714 opened Nov 5, 2025 by rmassei Contributor Loading…
2
Exploring the addition of groups and their purpose in YOLO configuration
#1687 opened Oct 14, 2025 by TuturBaba Contributor • Draft
1
ProTip! Adding no:label will show everything without a label.