Galactic Weekly: Week 9, 2026

Galactic Weekly

Summary

Repositories with activity: 21
New issues: 17
Issues closed: 33
PRs opened: 162
PRs merged: 87
Contributors: 49

Highlights

This week, 49 contributors merged 87 pull requests and closed 33 issues across 21 repositories. The Galaxy server received bug fixes in the workflow editor, markdown rendering, and data handling, along with enforcing storage quotas for Celery-based fetch jobs and making Tool Shed 2 the default. The Galaxy Hub website continued its migration from Gridsome to Astro, with removal of old framework code, CI updates, and fixes for server-side rendering issues, alongside new content about Galaxy for particle accelerators and Jetstream2 genome assemblies. The Training Material repository updated several tutorials for Galaxy 25.1+ compatibility and usability, while tools-iuc updated packages including Cutadapt, HyPhy, PretextMap, and mosdepth, and the IWC repository updated the metagenomics genes catalogue and RNA-seq differential expression workflows.

Most Active Repositories

Repository	PRs Opened	PRs Merged	Issues Opened	Issues Closed
galaxy	48	22	6	17
galaxy-hub	39	27	5	3
training-material	12	10	1	5
tools-iuc	17	5	1	2
iwc	12	4	0	1
usegalaxy-tools	6	1	2	1
gxy.io	3	3	0	0
galaxy_codex	4	2	0	0
galaxy-skills	3	2	0	0
gxformat2	2	2	0	0

Repository Summaries

galaxy-hub

This week’s work on galaxy-hub focused heavily on completing the migration from the Gridsome static site framework to Astro, including removing the old Gridsome site code, switching CI to Astro-only, and fixing several Vue server-side rendering hydration mismatches caused by date handling and apostrophes in titles. Infrastructure changes included renaming the default branch from master to main, adding CloudFront cache invalidation after S3 deploys, and enabling schema checking in CI. Content updates added news posts about Galaxy for particle accelerators and Jetstream2 genome assemblies, updated meeting details for the SPOC and Tool Development SIGs, added the microGalaxy roadmap, and included NFDI4BioImage annotations on news and events pages.

training-material

This week, the Galaxy Training Material repository received updates to several tutorials, including clarifications about nested collections in Galaxy 25.1+, updates to the RStudio in Galaxy tutorial, and a new tip in the Mapping tutorial about setting dbkey for samtools stats. Infrastructure changes included a fix to avoid rendering empty tool install files and redirects for Hall of Fame pages. The repository also added a news item for a misconceptions paper, a recommendation on citing public workflows, and updated persistent URLs and cached commit data, while closing out several issues related to tutorial usability and tool install rendering.

galaxy

This week’s changes to the Galaxy repository included several bug fixes across the workflow editor, markdown rendering, and data handling—such as fixing infinite request loops in cached stores, correcting collection step rendering in reports and markdown, repairing the “Create New” workflow editor state reset, and fixing dbkey filtering when the dbkey is unset. Storage quotas are now enforced for Celery-based data fetch jobs, and the Tool Shed 2 was made the default, with legacy Shed tests removed from CI. Other updates improved filesystem path construction (using os.path.join or pathlib.Path instead of f-strings), added shared XML formatting utilities to galaxy-tool-util, and refined the Type and Reference selectors in the Upload Activity.

gxformat2

This week, the gxformat2 repository merged two pull requests. One updated the minimatch dependency in the TypeScript portion of the project, and the other applied code formatting and linting to the Python codebase using the black and ruff tools.

tools-iuc

This week, the tools-iuc repository merged five pull requests: a fix for Cutadapt’s --minimum-length parameter default, a bug fix for HyPhy’s annotate invert behavior, an update to PretextMap with a new --highres flag, a Galaxy version bump for ToolDistillator, and an update of mosdepth from version 0.3.12 to 0.3.13. One new issue was opened regarding Samtools Stats not showing reference genomes, and two issues were closed, including that same Samtools Stats issue and a kraken2 bug involving incorrect datatype assignments for zipped input datasets.

galaxy-job-config-init

A pull request was merged that adds a --local-workers option, allowing users to specify the number of workers for the LocalJobRunner when generating Galaxy job configuration.

brc-analytics

This week, the brc-analytics repository closed four issues covering several areas: adding support for creating social media posts using the galaxy-social bot, adding a file with a landing request, improving the reliability of ENA (European Nucleotide Archive) integration, and adding a visualization for the variant calling workflow.

galaxy-language-server

This week, the repository updated the minimatch dependency in the client directory from version 3.1.2 to 3.1.4, addressing a known issue in that package. A separate pull request improved the setup process for the Python environment used by the project.

iwc

Two dependency packages (lodash-es/mermaid and minimatch) were updated in the website directory. On the workflow side, the metagenomics genes catalogue workflow was updated, and the RNA-seq differential expression workflow was updated from version 0.7 to 0.8. A test release issue for version 26.0 was also closed.

pulsar

A single pull request was merged this week, removing the project’s dependencies on distutils, pkg_resources, and stopit. These are older or deprecated Python libraries, and their removal updates Pulsar’s codebase to use more modern alternatives.

galaxy-k8s-boot

A single pull request was merged this week, containing adjustments based on testing of the galaxy-k8s-boot project. The specific tweaks address issues found during testing, though the details of the changes were not elaborated in the pull request title.

galaxy_codex

A new page was added with content for imaging.usegalaxy.org. The repository’s resources were also updated through an automated process.

usegalaxy-tools

A pull request was merged to add imaging tools from usegalaxy.eu to the repository. Two new requests were opened: one to increase compute resources for the optitype tool on usegalaxy.org, and another to install the qiime2 import-fastq tool on usegalaxy.org. A previously reported bug involving a permissions error in Funannotate predict was closed.

galaxy-skills

Two pull requests were merged this week. One added a new “tool-selection-diagram” sub-skill to the tool-dev skill area. The other fixed and updated the hub-news-posts skill based on lessons learned from actually creating posts.

gx-it-proxy

The Galaxy Project’s gx-it-proxy repository had one pull request merged this week, which bumped the version of the “minimatch” dependency. This is a routine dependency update, likely to incorporate bug fixes or security patches from the newer version of the library.

gxy.io

Three redirects and a new page were added this week. Redirects were set up for microbiology.usegalaxy.org and imaging.usegalaxy.org, and a welcome page was added for the Biodiversity lab.

usegalaxy-playbook

A pull request was merged this week that adds an Imaging theme and a tool view panel to the usegalaxy-playbook repository. This change introduces a dedicated visual theme and curated tool panel for imaging-related workflows in Galaxy.

total-perspective-vortex

A new issue was reported this week identifying a bug where linting fails for the tool.tool_type attribute. No other activity (pull requests, merges, or releases) was recorded for the repository during this period.

gravity

Two pull requests were merged this week in the Gravity repository. One added a dispatch option based on the Gunicorn version, and the other fixed an issue with version checking.

idc

A new issue was opened this week to discuss data documentation for the IDC (Intergalactic Data Commission) repository. No other activity such as pull requests, merges, or code changes was reported during this period.