Jennifer Hillman-Jackson

https://toolshed.g2.bx.psu.edu/repository?repository_id=997cccce43caabe7 Sub-sample sequences files e.g. to reduce coverage (Galaxy Version 0.2.5) Currently installed at https://usegalaxy.eu

Mpileup will need an update once corrected and in MTS

1

Problems described along with test history here: https://github.com/galaxyproject/tools-iuc/issues/1921

**Installed at both ORG/EU:** * MTS update 2018-12-12: **FIMO - Scan a set of sequences for motifs (Galaxy Version 4.12.0.0)** https://toolshed.g2.bx.psu.edu/view/iuc/meme_fimo/c1a9a297ba8b * MTS update 2018-5-17: **MEME - Multiple EM for...

Add PLAZA (plant) genomes to test, main, and cvmfs

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As discussed at prior GCC's and other places, getting plant genomes into Galaxy in an organized and consistent way across usegalaxy.* servers will address requests from users. The how-to for...

Update Mothur wrapped tools to version 1.40.5 once in MTS

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Tracking ticket, wrapper development still in progress by @shiltemann Will link WIP/PRs back as they become available.

Consider adding tool: Newick display to support users running GTN 16S tutorial on main

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MTS: https://toolshed.g2.bx.psu.edu/view/dcorreia/newick_display/3200899efad9 Tool: Newick display - Display a phylogenetic tree as SVG v1.6 Tutorial: http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html#otu-based-analysis Section: "Tree", the tool Newick display is used after Mothur "Tree.shared Generate a newick tree...

**Ephemeris**: Specifically, functions for batch data fetch/index with `run-data-managers` - https://github.com/galaxyproject/ephemeris - https://ephemeris.readthedocs.io/en/latest/commands/run-data-managers.html @nate This is how we should install genomes/indexes going forward, agree? @jmchilton @bgruening Ready yet or wait...

MultiQC does not recognize raw data (txt) from FastQC when in a collection

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**Problem:** The select menu does not find the FastQC collection input. However, it will find other ~collections~ individual dataset with the txt datatype. Both tool versions impacted and was not...

Increase memory for Mothur tools

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Use case: https://biostar.usegalaxy.org/p/23685/#25087

FTP batch upload failures

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Tracking ticket to share with the community as needed. The corrections are in progress. When done, this ticket will be closed out. **Problem:** A few, but not all, datasets queued...