Jennifer Hillman-Jackson

Pull these from EU to ORG

**Scope** Now re data - [ ] Migrate what EU has to CVMFS or ORG (+AU?) indexes * Total of four exist so far Prep for larger indexing projects -...

Confirm if Heatmap fixed or not

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https://github.com/galaxyproject/galaxy/issues/3030

Extract Genomic DNA versions 3.x+ do not link with built-in genome indexes

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**Workaround for end-users:** > Please use **bedtools GetFastaBed** instead. It performs the same basic function plus has more options. **Tool:** Extract Genomic DNA using coordinates from assembled/unassembled genomes (Galaxy Version...

Test taxonomy_krona_chart 2.7.1

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Testing all Krona - [x] https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1 - [x] https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 - [x] https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1 - [x] https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0 Generates an input for Krona - [x] https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.2

We could copy all or just the most recent (2020+). Ping @natefoo @bgruening -- I know Nate was doing this for other tool indexes. How can I help?

Reported to galaxy-bugs 2022-02-08 * Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results/0.1.1 * Tool test (failed): https://github.com/mvdbeek/usegalaxy-tests/issues/14 * The tool is at the most current version in the MTS: https://toolshed.g2.bx.psu.edu/repository?repository_id=4c6cf49fac204b74 Update: Also fails at...

Reported to galaxy-bugs 2022-02-08 * Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/ebi_metagenomics_run_downloader/ebi_metagenomics_run_downloader/0.1.0 * Tool test (failed): https://github.com/mvdbeek/usegalaxy-tests/issues/13 * The tool is at the most current version in the MTS: https://toolshed.g2.bx.psu.edu/repository?repository_id=3dbb223c1d6a210d Update: is a tool...

> Workaround for end-users: > > Modify the dataset names of the inputs so that each is distinct. Pencil icon > Edit Attributes > first tab > Name > edit...

"Apply Rule to Collection" -- py3 related?

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**Tool:** Apply Rule to Collection (Galaxy Version 1.0.0) **Tutorial:** Problem at step 7 here: https://galaxyproject.github.io/training-material/topics/galaxy-data-manipulation/tutorials/upload-rules/tutorial.html#apply-rules-to-existing-collections **Reported at Galaxy Help:** https://help.galaxyproject.org/t/problem-applying-regular-expression-wrong-number-of-groups-found-in-tutorial-collections-rule-based-uploader/2915 **Reproducible:** https://usegalaxy.org/u/jen/h/test-coll **Screenshots** Set it up: Review: Submit: ...job submission...