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Last updated 12-11-17

Check individual linked tickets to review the most current status for any known issue

Working at Galaxy Main

Server-specific issues:

Issue by tool name

  1. (15) Heatmap 1.0.0 Missing dependencies. Impacts Galaxy Main Details:
  2. (2 bugs +github) CummeRbund 1.0.1 Select for "gene_id" problematic. Graphs for Heatmap and Volcano plots also problematic. Impacts Galaxy Main Details:
  3. (1) SnpEff Download v4.1.0 and 4.3k.0. Index problem for certain databases nested in .zip archives from the source. Impacts Galaxy Main Details:
  4. (many) Upload Retested 6/1/17 v 17.05 then again on 10/18/17 v 17.09 on Main. Still assigning "pileup" as autodetected datatype in a greedy way for tabular format data that has a variable numbers of columns per line. Impacts Galaxy Test and Main Details:
  5. Rerun Function (many tools) Rerun view for grey "new" status dataset, and sometimes green successful datasets, fails to open Advanced Options on reloaded tool form. Impacts Galaxy Main Details:
  6. (many) Htseq-count 0.6.1galaxy3 Does not report standardized memory failure error message. Suggested improvements are in the ticket. Impacts Galaxy Main Details:
  7. (a few) Featurecounts Is being updated from 1.4.6.p5 to 1.5.3 to address a bug is but not in the MTS yet (was just upgraded). Update Main once in MTS and test. Impacts Galaxy Main Details:

retest/status in progress

  1. (1) Annovar 0.2 Wrapper problems. Use v 0.1 as a workaround. Impacts Galaxy Main Details:
  2. (1) Picard SamToFastq 1.136.0 Does not list fastqsanger output datasets in Workflow editor. Impacts Galaxy Main and a local Galaxy (not tested on Cloudman). Details:
  3. (?) BWA-MEM produces BAM that fails ValidateSamFile 1.136.0. Default options for both. ValidateSamFile tool needs tuning? Impacts Galaxy Main Details:

Note: (N) is number of confirmed bug reports about issue. Not all issues can be counted this way. Count of (many) indicates that this is ongoing user problem with usage, often clarified when reviewing other bug reports/questions.

Tools that need updated usage/help

Fixed pending server update

  1. (many) StringTie 1.3.3. Errors when output for DEseq2/EdgeR is selected. Impacts Galaxy Main Details and workaround: Status:

Integration tests in progress ( v 17.09 )


  1. (21) MEME Has dependency issues. Updates have not resolved usage problems yet (tool has never worked). Impacts Details:
  2. Needs RE-TEST (many) Upload (across releases) Trailing return characters in pasted data cause problems and the "why" is not clear to users. Impacts Galaxy Main, locals, cloud. Details:
  3. Needs RE-TEST (many) MAF tools 1.0.1 Switching between MAF data sources does not refresh tool form/dbkey list. Impacts Galaxy Main Details:


  1. Needs RE-TEST (many) 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:
  2. 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:

Issue by user interface behavior

  1. 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:

Issue with performance at Galaxy Main

  1. 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:
  2. 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.

Issue by error message

  1. Error from a tool in the NGS: SAMtools or NGS: Picard groups about sort order.
  2. Tool is failing for memory or walltime (click on bug icon to review - this does not need to be submitted).
  3. Tool is failing for what appears to be a cluster error.
  4. Tool is failing and you are not sure what the error message means or how to troubleshoot/get help.

Try this first: Sort your inputs

Check all inputs: All Support help

If you cannot determine the problem from the help above, the bug report can be sent in: Common tool errors and solutions, including how to send in a bug report.

Correction Completed History

  1. Convert BIOM Dependency issues (now resolved). Impacts Galaxy Main Details:
  2. Workflows Multiple input modifications within the editor triggers a browser crash. Impacts Galaxy Main (and potentially other Galaxy flavors). Details:
  3. Upload Fixed early 2017. Tool was problematically padding spaces to tabs when number of pasted columns varies. Impacts Galaxy Main Details:
  4. Uniprot Dependency fix on 5/15/17. Impacted Galaxy Main, locals, cloud (any install). Details:
  5. Megablast 1.2.0. Fails for configuration error. Metagenomic alternative: Kraken. Impacts Galaxy Main Details:
  6. Freebayes 0.4.1 + Now requires upsteam inputs have database metadata assigned - see ticket for workaround. Impacts Galaxy Main Details:
  7. Du Novo: Align families 0.7 Tool updates removed the cluster targetting for Jetstream. Fix made (increased allocated resources at target clusters). Impacts Galaxy Main Details:
  8. Kraken 0.10.6, Krona pie chart from taxonomic profile 2.6.0, Convert Kraken data to Galaxy taxonomy representation 1.1 Missing dependencies, some localized to the roundup cluster (default). Resolved in updated tools and versions (Kraken 1.2, Krona 2.6.1). Impacts Galaxy Main
  9. GenomeDiversity PrepareInput gd_prepare_population_structure 1.1.0 Dependency/config issue resolved 1.2.0. Impacts Galaxy Main Details
  10. DEXseq 1.20.1 Dependencies issues. Related tool DEXSeq Counts 1.20.1 already has fixed dependency issue. Impacts Galaxy Main Details:
  11. MACS2 bdgdiff + bdgbroadcall Tool version updated 4/11/17 errors with "macs2 command not found". Impacts Galaxy Main Details:
  12. MACS2 bdgdiff Did not have "Versions" menu on tool form. Cannot change versions on tool form still, but closed out anyway. Impacts Galaxy Main http://usegalaxyorg. Details:
  13. Cuffmerge v 2.2.1 Older v 0.0.6 is successful with same inputs. Closed unless reported again. Impacts Galaxy Main Details: Might be related to
  14. DEXseq Count 1.20.1 Dependencies issues. Primary tool DEXSeq may also have the problem, but since the upstream tool is non-functional, it cannot be tested on Main. Impacts Galaxy Main Details:
  15. Deseq2 2.11.38 MTS update to 2.11.39 fixes dependency issues. Impacts Galaxy Main Details:
  16. Deprecated tool Draw phylogeny 1.0.0 Version 1.0.0 has a dependency issue. Impacts Galaxy Main Details:
  17. Diffbind 2.2.0/2.1.0 Dependency problems fixed in 2.2.0 Impacts Galaxy Main Details:
  18. Salmon 0.7.2 Fails with a specific error message due to tool dependency problems. The updated tool version 0.8.2 resolved the problem. Impacts Galaxy Main Details:
  19. Deep Tools correctGCBias Unrecognized arg --filterOut produces an error. Impacts Galaxy Main but is core tool issue. Details:
  20. Deep Tools multiBamSummary Doesn't always produce output. Impacts Galaxy Main Details:
  21. Tophat Tool is being deprecated and no longer runs on Jetstream (where original metadata problem was from). Impacts Galaxy Main Details:
  22. MAF tools 1.0.1 Fix made for legacy env updates. Extract Pairwise MAF blocks 1.0.1 GeneBed_Maf_Fasta2. ( Tool Extract Pairwise MAF blocks may also need fix. Impacts Galaxy Main, locals, cloud.
  23. Trimmomatic Update to version 0.36.3 corrected tool form option "Illumina Clip" failures. Impacts Galaxy Main Details:
  24. Picard Tool: CollectRnaSeqMetrics 1.136.0 Impacts Galaxy Main Original Details: Still fails with updated tool version 1.136.0. Update: Error due to input format - is very specific and needs to be clarified on tool form, see ticket.
  25. MarkDuplicatesWithMateCigar 1.126.0 Problem with tool form option specific to version 1.126.0. Repo updated to version 1.136.0 and now works at Main. Impacts Galaxy Main Details:
  26. Trackster and GFF/GTF datasets Fail to load with a specific error. Impacts Galaxy Main Details:
  27. EBI SRA Main 1.0.1 Tool errors when loading .bz2 compressed data from the "Submit files (galaxy)" link. Details and workaround:
  28. Trackster and BED datasets Fail to load with a specific error. Impacts Galaxy Main Details:
  29. GenomeSpace import (genomespace_file_browser_prod). Potential run-time issues. Impacts Galaxy Main Details:
  30. DESEQ2 Fails after tool update - new error message in linked ticket. Impacts Galaxy Main Details: Might be related to
  31. MACS2 Callpeak Errors out but job produces result data (in red datasets). Impact Galaxy Main and possibly other installs. Details:
  32. MACS2 CallPeak This tool has a current known issue with the option Fold Enrichment. Impacts Galaxy Main Details:
  33. 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:
  34. 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)
  35. Convert Formats: Convert BAM to ScIdx Fails for dependency issue. Impacts Galaxy Main Details:
  36. Group Fails under specific conditions. Fixed, pending deployment. Impacts Galaxy Main Details:
  37. Multi-join Has dependencies issues. Impacts Galaxy Main Details
  38. GenomeDiversity Admixture gd_specify 1.1.0 Dependency/config issue corrected on server, no version change, retested after other GD 1.2.0 tools updated = pass. Impacts Galaxy Main Details
  39. BAMTools Convert, Merge, Randomize Fails for Convert to Bed + Yaml. Impacts Galaxy Main Details:
  40. VCF-VCFintersect Needs to be updated in the Main Tool Shed and Galaxy Test/Main servers. Impacts Galaxy Main Details:
  41. Bedtools SpacingBed Dependency/config issues. Impacts Galaxy Main Details
  42. 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:
  43. Duplicates in UI Display of Tabular Datasets Fixed, pending deployment. Impacts Galaxy Main and all other Galaxy flavors. Details:
  44. Multi-join Frozen tool form options (related to icon display, see linked issues in ticket). Impacts Galaxy Main Details:
  45. Fetch Alignments/Sequences MAF tools have a dependency issue. Impacts Details:
  46. Summary Statistics Fails for dependency issue. Impact Details:
  47. CloudMap: "Hawaiian Variant Mapping with WGS" Dependency issues. Impacts Galaxy Main Details:
  48. HISAT2 Fails, updating tool repo version on Main in progress. Impacts Details:
  49. Tophat Execution with a single fastq file (unpaired) produces an error. Wrapper or dependency issue. Impacts Details:
  50. Picard Tool: ValidateSamFile Errors (as a green successful dataset) in summary mode. Impacts Galaxy Main Details:
  51. FastQC, MACS2 HTML results do not display when "eye" icon used. Impacts Galaxy Main Details:
  52. 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:
  53. CollectAlignmentSummaryMetrics Fixed on Main at version 1.136.0.