tools-iuc

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Tool update: featureCounts

2

Hi All, today while running the following [GTN tutorial](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html), we discovered a not user-friendly behavior of how [FeatureCounts](https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts) allows users to use the build in references. The tutorial asks to:...

teresa-m

FOR CONTRIBUTOR: * [x] I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. * [ ] License permits unrestricted use (educational + commercial) *...

paulzierep

https://github.com/Jerrythafast/

bgruening

SRST2 has incorrect format on discover datasets outputs.

3

``` $ ag discover_datasets.*format.*, tools/srst2/srst2.xml 200: ``` srst2 is the only tool to use a format with a `,` which seems incorrect, as the file gets marked 'binary or unknown'...

hexylena

Binsize is currently in a form repeat with default length of 1 and a single default value so it always appears on the command line - there is no way...

fubar2

Updating tools/augustus to 3.5.0

4

This PR updates the Augustus tool with addition of new species and updates to the test data Fixes: https://github.com/galaxyproject/tools-iuc/pull/6433 --- FOR CONTRIBUTOR: * [x] I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document...

SaimMomin12

Updating tools/scater from version 1.22.0 to 1.30.1

4

Hello! This is an automated update of the following tool: **tools/scater**. I created this PR because I think the tool's main dependency is out of date, i.e. there is a...

planemo-autoupdate

Updating tools/bbtools from version 39.08 to 39.26

14

Hello! This is an automated update of the following tool: **tools/bbtools**. I created this PR because I think the tool's main dependency is out of date, i.e. there is a...

gxydevbot

better label

2

FOR CONTRIBUTOR: * [x] I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. * [x] License permits unrestricted use (educational + commercial) * [...

nilchia

JupyLab Tool Issues

11

JupyLab/Jupyter tool issues collected from 2024 Bioinfo Bootcamp preparation and trying to get these tutorials to work after updates: Please see notes here about get/put issues & installation issues &...

nomadscientist