Cameron Hyde

New tool Hapcut2

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)...

Add tool GTDB-Tk

1

For metagenomics classfication of bacteria/archaea. Requested in [microGalaxy tools](https://github.com/orgs/galaxyproject/projects/24/views/1).

Jackhammer / stockholm.c "No space left on device"

2

Related to https://github.com/deepmind/alphafold/issues/280. We are getting a disk write error after Jackhammer completes: ``` I0613 00:13:04.128991 139887425492800 utils.py:36] Started Jackhmmer (uniref90.fasta) query I0613 01:04:43.969136 139887425492800 utils.py:40] Finished Jackhmmer (uniref90.fasta) query...

Infer collection element naming with `default_identifier_source`

6

# The issue When collections are created as a tool output, the Galaxy tool author can declare output element names by referencing input datasets. However, this feature is poorly documented...

Hard-coded database source for GTDB data manager

1

The DB URL field should might be better as a `select` field, with hard-coded values. That way admins will easily be able to select the appropriate version to download, and...

Quickmerge fails to set its PATH internally

6

Hi, I am developing a Galaxy tool for Quickmerge and it looks like your tool is doing some internal PATH management that causes an edge-case bug. When I `conda install...

Per-host configuration ignored for some hostnames

6

Relates to "per-host configuration" of Galaxy: https://github.com/galaxyproject/galaxy/pull/12328 **Galaxy Version and/or server at which you observed the bug** Galaxy Version: 23.2.1.dev0 https://dev.gvl.org.au/ Commit: 8bda304592e448510470ba94594ee64357d969c4 I am trying to set the `default_panel_view`...

Tool request: FGBio suite

1

See: https://github.com/fulcrumgenomics/fgbio > A set of tools to analyze genomic data with a focus on Next Generation Sequencing. Currently available in the toolshed: - [FastqToBam](https://toolshed.g2.bx.psu.edu/view/jjohnson/fgbio_fastq_to_bam/6137ff37bea1) - [GroupReadsByUmi](https://toolshed.g2.bx.psu.edu/view/jjohnson/fgbio_group_reads_by_umi/9efbd847e5d1) We would like...

Drag-and-drop (and related) history issues

1

**Describe the bugs** Drag-and-drop between histories mostly works (allowing for for issue #15361) but I notices a few minor issues. This is all done in side-by-side history view: 1. Drag-and-drop...

Genome list page

11

@ElectronicBlueberry Add a client route `/genome-list` to display a list of available genomes, reusing components from the `/datatypes` page. Allows sorting and keyword filtering. ## How to test the changes?...