Galactic Weekly: Week 12, 2026

Galactic Weekly

Summary

Repositories with activity: 19
New issues: 53
Issues closed: 61
PRs opened: 169
PRs merged: 94
Contributors: 51

Highlights

This week, 51 contributors merged 94 pull requests across 19 repositories. The main Galaxy codebase received workflow editor improvements—including a new “Isolate” focus mode and a step input/output toggle on the invocation graph—along with bug fixes backported to the 25.1 and 26.0 release branches, corrected binary unit prefixes throughout the codebase, and a new Playwright-based test suite for running tool tests through the UI. The gxformat2 library fixed several workflow round-tripping bugs and modernized its build tooling by migrating to pyproject.toml and uv dependency groups. Across other repositories, tools-iuc updated several tool versions (snpSift, NCBI Datasets, inferCNV, GeoPandas, Pretext), the Galaxy Hub added a “Cite Galaxy” section and new event entries, and the training-material repository updated contributor records and tutorial content.

Most Active Repositories

Repository	PRs Opened	PRs Merged	Issues Opened	Issues Closed
galaxy	56	27	33	40
galaxy-hub	18	14	2	0
gxformat2	13	12	6	7
tools-iuc	16	9	4	4
training-material	10	10	0	0
iwc	22	1	2	0
brc-analytics	7	7	4	8
usegalaxy-tools	7	7	1	2
galaxy_codex	7	0	0	0
galaxy-language-server	2	2	0	0

Repository Summaries

usegalaxy-tools

This week, several new tools were added to the usegalaxy-tools repository, including IDR Download, Omero tools, fastga (in the Assembly section), and an updated kmindex wrapper. Routine updates were applied to cloud and general tool repositories, and IWC tools were installed for the cloud instance. A new issue was opened regarding a configuration problem with snippy 4.6.0, while two older issues requesting increased memory allocation for snippy and snippy_core were closed.

tools-iuc

This week, the tools-iuc repository merged nine pull requests, mostly consisting of tool version updates: snpSift was updated to 5.4.0c, NCBI Datasets to 18.21.0, inferCNV from 1.22.0 to 1.26.0, GeoPandas from 1.1.2 to 1.1.3, and Pretext was also updated. Additional changes included adding tool-data tables to HapCut2, adding help text for arithmetic expressions in the Column Maker tool, and updating a default parameter for kmindex. Four issues were opened—covering a new output request for chewBBACA, Trimmomatic quality encoding detection, a proposed multi-genome alignment workflow, and a CI file-not-found error—while four issues were closed, including the CI error and fixes related to NCBI Datasets.

gxformat2

This week, gxformat2 received several bug fixes addressing issues with workflow round-tripping, including fixes for unlabeled tool steps producing dangling numeric source references, step labels containing / breaking source reference parsing, and unwanted synthetic labels being assigned to unlabeled input steps. New features were added for bidirectional workflow comment conversion, pick_value support in the Format2 schema, and handling of unencoded tool_state in native workflows. The project also underwent build and development tooling modernization, migrating from setup.py to pyproject.toml, adopting uv dependency groups for linting/testing/type-checking, and replacing the deprecated distutils with the packaging library in release scripts.

brc-analytics

This week, the brc-analytics repository added new workflows for freebayes and braker3 (variant calling and gene annotation), and restricted certain workflows to only appear for assemblies that have a Galaxy data cache available. The “Analyze in Galaxy” flow was simplified, workflow taxonomy filters were reworked to use human-friendly species and lineage selection, and a carousel card was added to solicit user feedback via a survey. The version was bumped to 0.25.0, and several issues were closed related to diploid variant calling workflow registration, assembly updates, and workflows previously stuck in a “Coming Soon” state.

training-material

This week, the Galaxy Training Material repository updated contributor records by adding Arthur Barreau and Nadine Le Bris and making other contributor file changes. Several tutorials were edited, including tweaks to the Introduction to Galaxy for Research Data Management tutorial, a parameter fix, and unification work on the SFB992 materials. The GTA2026 event page was updated with a registration link and track information, missing data-library.yaml files were added, and persistent URL references were updated twice.

galaxy-hub

This week, the galaxy-hub repository received updates to the homepage and welcome page to add a “Cite Galaxy” section, along with fixes to the citing-galaxy page. Several event-related changes were made, including a new event entry for a DHXpresso webinar, a GTA25 banner, and additions to the BHEU24 event page. Maintenance work included multiple syncs from the training-material repository, fixes to GTN import slug normalization and casing errors, contributor unification for SFB992/CRC992, removal of a fellowship application, and additions of GTN badges for organisations and affiliation labels. Two new issues were filed regarding broken links on the events page and minor mobile display problems.

galaxy-language-server

This week’s activity consisted of two dependency update pull requests. The client-side flatted package was bumped from version 3.2.4 to 3.4.2, and five server-side dependencies were updated as a group. No feature changes or bug fixes were included.

planemo

A single pull request was merged this week, fixing a bug where the workflow linting feature would crash if a tool’s state was stored as a dictionary rather than a JSON string.

iwc

A dependency update was merged, bumping the h3 package from version 1.15.5 to 1.15.8 in the website directory. Two new issues were opened: one reporting connection validation failures, and another requesting that the IWC logo be added to the global Galaxy Project branding page.

galaxy

This week, the Galaxy repository received UI and workflow editor improvements, including a new “Isolate” focus mode for the workflow graph, a toggle to view step inputs/outputs on the invocation graph, a copy link button on published workflow pages, and a change stack count indicator on the workflow editor. Several bug fixes were backported to the 25.1 and 26.0 release branches, addressing issues such as race conditions during deletions, paused job queuing, redundant empty collection elements, unhandled exceptions in tool form population, and collection update locking.

On the technical side, binary unit prefixes were corrected from MB/GB to KiB/MiB/GiB throughout the codebase, a batch Celery task was added for history dataset purging, and a new Playwright-based test suite was introduced for running tool tests through the tool form UI. New issues filed this week cover topics including hidden

gxy.io

A single pull request was merged this week, adding the URL for the GTA2026 (Galaxy Training Academy 2026) registration form to the site.

galaxy-k8s-boot

A new application for monitoring Galaxy pod usage on Kubernetes was added to the repository. This was the only change merged this week.

gxadmin

Two pull requests were merged into gxadmin this week. One added a new query that retrieves the n_live_tup (estimated number of live rows) from PostgreSQL’s pg_stat_user_tables. The other added a mutate query that triggers analysis on tables that have not yet been analyzed.

gxabm

A new issue was opened proposing the addition of a “tools” subcommand to the gxabm repository. No other activity (pull requests, merges, or releases) was reported for the week.