Issue by tool name

  1. SamToFastq Does not list fastqsanger output datasets in Workflow editor. Impacts Galaxy Main and a local Galaxy (not tested on Cloudman). Details:
  2. Draw phylogeny Version 1.0.0 has a dependency issue. Impacts Galaxy Main Details:
  3. Freebayes Now requires upsteam inputs have database metadata assigned. This breaks some older workflows and published tutorials. Impacts Galaxy Main Details:
  4. DESEQ2 Fails after tool update - new error message in linked ticket. Impacts Galaxy Main Details: Might be related to
  5. GenomeSpace import (genomespace_file_browser_prod). Potential run-time issues. Impacts Galaxy Main Details:
  6. MarkDuplicatesWithMateCigar Problem with tool form option. Impacts Galaxy Main Details:
  7. Cuffmerge v 2.2.1 Older v 0.0.6 is successful with same inputs. No changes to tool wrapper, but is now failing. Problem with selecting multiple input files? Impacts Galaxy Main Details: Might be related to
  8. Heatmap 1.0.0 Missing dependencies. Impacts Galaxy Main Details:
  9. Upload Trailing return characters in pasted data cause problems. Impacts Galaxy Main, locals, cloud. Details:
  10. Htseq-count Does not report standardized memory failure error message. Impacts Galaxy Main Details:
  11. MAF tools Switching between data sources does not refresh tool form/dbkey list. Impacts Galaxy Main Details:
  12. BWA-MEM default options produces BAM that fails ValidateSamFile. Default options for both. New ValidateSamFile tool likely needs tuning. Impacts Galaxy Main Details:
  13. Fetch Alignments/Sequences Tool group. Toggle between sources does not refresh genome list on tool form. Impacts Galaxy Main Details:
  14. Diffbind Produces green empty datasets with dependency issues. Impacts Galaxy Main Details:
  15. MACS2 Callpeak Errors out but job produces result data (in red datasets). Impact Galaxy Main and possibly other installs. Details:
  16. MACS2 CallPeak This tool has a current known issue with the option Fold Enrichment. Impacts Galaxy Main Details:
  17. MACS2 bdgdiff Produces green emtpy datasets for all output options . Impacts Galaxy Main Details:
  18. EBI SRA Tool errors when loading .bz2 compressed data from the "Submit files (galaxy) link. Details and workaround:
  19. Trackster and BED datasets Fail to load with a specific error. Impacts Galaxy Main Details:
  20. Picard Tool: CollectRnaSeqMetrics Impacts Galaxy Main Original Details: Still fails with updated tool version 1.136.0.
  21. MEME Likely has dependency issues. Update on Main pending. Impacts Details:

Re-test to confirm correct at

Fix or enhancement, but not yet implemented at

  1. Needs main update (new repo Deep Tools correctGCBias Unrecognized arg --filterOut produces an error. Impacts Galaxy Main but is core tool issue. Details:
  2. Needs main update (new repo same as above) Deep Tools multiBamSummary Doesn't always produce output. Impacts Galaxy Main Details:
  3. PASS on Test, needs Main update Upload Problematically padding spaces to tabs when number of pasted columns varies. Impacts Galaxy Main Details:
  4. Upload Is assigning "pileup" as autodetected datatype in a greedy way for tabular format data. Impacts Galaxy Test and Main Details:

Recently corrected/implemented at

  1. NCBI SRA Tools Dependency/config issue resolved, but tool version mismatch for wrapper on Main. Smaller files working on a local, but not Main. Work-around: Use "Get Data > EBI SRA" or download from NCBI/FTP to Galaxy. Impacts Galaxy Main Details:
  2. Deeptools Fails for a specific error. Tool has been revised and pending upgrade. Impacts Galaxy Main Details and link to work-around posted at Galaxy Biostars: Other issues with tool at Galaxy Main, perhaps global (see ticket)
  3. Convert Formats: Convert BAM to ScIdx Fails for dependency issue. Impacts Galaxy Main Details:
  4. Group Fails under specific conditions. Fixed, pending deployment. Impacts Galaxy Main Details:
  5. Multi-join Has dependencies issues. Impacts Galaxy Main Details
  6. GenomeDiversity Admixture Dependency/config issue. Impacts Galaxy Main Details
  7. BAMTools Convert, Merge, Randomize Fails for Convert to Bed + Yaml. Impacts Galaxy Main Details:
  8. VCF-VCFintersect Needs to be updated in the Main Tool Shed and Galaxy Test/Main servers. Impacts Galaxy Main Details:
  9. Bedtools SpacingBed Dependency/config issues. Impacts Galaxy Main Details
  10. Tophat Fails for a specific use case. Update to v 2.1.0 may solve (update: did solve). Also covers tool form option modeling. Impacts Galaxy Main Details:
  11. Duplicates in UI Display of Tabular Datasets Fixed, pending deployment. Impacts Galaxy Main and all other Galaxy flavors. Details:
  12. Multi-join Frozen tool form options (related to icon display, see linked issues in ticket). Impacts Galaxy Main Details:
  13. Fetch Alignments/Sequences MAF tools have a dependency issue. Impacts Details:
  14. Summary Statistics Fails for dependency issue. Impact Details:
  15. CloudMap: "Hawaiian Variant Mapping with WGS" Dependency issues. Impacts Galaxy Main Details:
  16. HISAT2 Fails, updating tool repo version on Main in progress. Impacts Details:
  17. Tophat Execution with a single fastq file (unpaired) produces an error. Wrapper or dependency issue. Impacts Details:
  18. Picard Tool: ValidateSamFile Errors (as a green successful dataset) in summary mode. Impacts Galaxy Main Details:
  19. FastQC, MACS2 HTML results do not display when "eye" icon used. Impacts Galaxy Main Details:
  20. Trim leading or trailing characters Fails when option to specify input is fastq is used. Impacts Galaxy Main and possibly locals running 16.04. Details and workaround:
  21. CollectAlignmentSummaryMetrics Fixed on Main at version 1.136.0.

Issue by error message

  1. Error from a tool in the NGS: SAMtools or NGS: Picard groups about sort order. See: Sort your inputs

Issue by user interface behavior

  1. Rerun Function (many tools) Rerun view for grey "new" status dataset fails to open Advanced Options on reloaded tool form. Impacts Galaxy Main Details:
  2. Tophat (And potentially other tools). The Jetstream cluster may produce output datasets reporting problematic metadata. Current workaround: Expand the dataset by clicking on the name and reset metadata with the link provided in the yellow box. Impacts Galaxy Main Details:
  3. Workflows Multiple input modifications within the editor triggers a browser crash. Impacts Galaxy Main (and potentially other Galaxy flavors). Details:
  4. Reference Genome Missing from tool First, make certain that the dataset has the "database" metadata asssignment. If still missing, the genome may be undergoing indexing ( on Test, to be promoted to Main ). Check the details ticket below for notes and progress. If you do not see your genome, request it as instructed in the ticket. Remember that a Custom Reference Genome can be used right now instead for most tools. Impacts Bowtie2 Tophat(2) BWA BWA-MEM Kraken. Details:

  5. Workflows NOTE that a new workflow form is pending and these usage issues will be re-tested. Behavior: Reference genome selection at runtime or changes through editor are not persistent or do not allow use of a Custom Reference Genome/Build. Known issues, sometimes linked to specific tools (SAMTool, Tophat). Impacts Main Details:

  6. Pileup datasets not recognized by downstream tools. This is due to tabular datatype assignment by Mpileup/Generate pileup (SAMTools). Assignment of both start and end to the same column could be why auto-assignment of type is not possible. Workaround: Click on dataset's pencil icon and assign pileup datatype. Details:

  7. If there are issues with delays, reports of histories not loading, a blue screen stating that Galaxy is busy ... then check the Galaxy Status page to see if there is a problem with the server first:

  8. If status is OK, then read recent posts at Galaxy Biostars, where transient issues are often reported and clarified. A new question can be asked if there is no activity about the problem.