Issues

• Enhancement: orthofinder gene trees, somehow return all results and do not fail a larger job with many outputs

  galaxyproject/tools-iuc#8482 · Filter by author jennaj opened on Oct 3, 2026

• PICRUSt2 tools failing with blank input parameters when multiple file inputs are required

  galaxyproject/tools-iuc#8449 · Filter by author sakhabtoosh97-collab opened on Sep 22, 2026
  1

• Enhancement: Adjust Panaroo to interpret collection data correctly (add ".gff" to input file or element identifiers)

  galaxyproject/tools-iuc#8448 · Filter by author jennaj opened on Sep 21, 2026

• jbrowse: test 8 depends on all_fasta having exactly one entry, so it cannot pass outside CI

  galaxyproject/tools-iuc#8429 · Filter by author afgane opened on Sep 17, 2026

• Add remag

  tool request
  galaxyproject/tools-iuc#8413 · Filter by author bernt-matthias opened on Sep 11, 2026

• hyphy_fel: job exits 1 with no diagnostic — stderr contains only ignored OpenMPI warnings

  galaxyproject/tools-iuc#8392 · Filter by author afgane opened on Sep 5, 2026

• kmindex query: multi-index ("all indices") query fans out to thousands of per-shard datasets with no aggregated output

  galaxyproject/tools-iuc#8389 · Filter by author nekrut opened on Sep 3, 2026

• Data Manager table values should identify data, not installation time

  galaxyproject/tools-iuc#8360 · Filter by author mvdbeek opened on Aug 28, 2026
  3

• [Tool] ViReMa (Virus Recombination Mapper) — bioconda recipe stuck at 0.6/python2 while upstream is at 0.33

  tool request
  galaxyproject/tools-iuc#8326 · Filter by author QuandongPan opened on Aug 19, 2026
  1

• Additional output for Stacks2: population

  galaxyproject/tools-iuc#8323 · Filter by author igormakunin2 opened on Aug 18, 2026

• sra_tools: /http/timeout/read = "1000" in wrapper configfile sets a 1-second HTTP read timeout

  galaxyproject/tools-iuc#8316 · Filter by author pauldg opened on Aug 14, 2026

• Call for Support: Updating outdated metagenomics tools on IUC

  microGalaxy
  galaxyproject/tools-iuc#8301 · Filter by author SaimMomin12 opened on Aug 11, 2026
  9

• Warning: TargetFinder stderr messages like "Use of uninitialized value $offset in substr at /usr/local/bin/targetfinder.pl line 537"

  galaxyproject/tools-iuc#8165 · Filter by author jennaj opened on Jul 6, 2026
  1

• Tool request: OpenFold3

  tool request
  galaxyproject/tools-iuc#8144 · Filter by author B0r1sD opened on Jun 26, 2026
  4

  

• CI setup for ITs

  galaxyproject/tools-iuc#8137 · Filter by author bernt-matthias opened on Jun 25, 2026

• BayeScan tool : Define additional output files in the XML to enable workflow integration

  galaxyproject/tools-iuc#8131 · Filter by author GINAMO-EBVs opened on Jun 22, 2026
  3

• bug for FCS-GX

  galaxyproject/tools-iuc#8065 · Filter by author jaredbernard opened on Jun 4, 2026
  1

• Corrections for kaiju_kaiju 1.10.1+galaxy1

  galaxyproject/tools-iuc#8045 · Filter by author jennaj opened on May 29, 2026
  4

  

• hicup failing when there is a period in a genome name (like a versioned accession)

  galaxyproject/tools-iuc#7999 · Filter by author scottcain opened on May 18, 2026
  4

• Add graceful termination with fallback for maxbin2

  galaxyproject/tools-iuc#7986 · Filter by author paulzierep opened on May 13, 2026
  3

• Remove .lint_skip files from tools

  galaxyproject/tools-iuc#7890 · Filter by author SaimMomin12 opened on Apr 14, 2026
  

• picurst_pipeline crash

  galaxyproject/tools-iuc#7888 · Filter by author bgruening opened on Apr 13, 2026

• sceasy convert tool doesn't support seurat v5 format

  galaxyproject/tools-iuc#7884 · Filter by author Droslj opened on Apr 13, 2026
  7

• Tool for parsing the metadata of datasets as parameter values

  galaxyproject/tools-iuc#7875 · Filter by author kostrykin opened on Apr 10, 2026
  1

• MultiQC grep lookaheads on large inputs cause grep failure

  galaxyproject/tools-iuc#7865 · Filter by author natefoo opened on Apr 6, 2026