Issue by tool name

  1. SamToFastq Does not list fastqsanger output datasets in Workflow editor. Impacts Galaxy Main http://usegalaxy.org and a local Galaxy (not tested on Cloudman). Details: https://github.com/galaxyproject/tools-devteam/issues/414
  2. Draw phylogeny Version 1.0.0 has a dependency issue. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3158
  3. Freebayes Now requires upsteam inputs have database metadata assigned. This breaks some older workflows and published tutorials. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/409
  4. DESEQ2 Fails after tool update - new error message in linked ticket. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-iuc/issues/988 Might be related to https://github.com/galaxyproject/galaxy/issues/2989
  5. GenomeSpace import (genomespace_file_browser_prod). Potential run-time issues. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-iuc/issues/1010
  6. MarkDuplicatesWithMateCigar Problem with tool form option. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/401
  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 http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2989 Might be related to https://github.com/galaxyproject/tools-iuc/issues/988
  8. Heatmap 1.0.0 Missing dependencies. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3030
  9. Upload Trailing return characters in pasted data cause problems. Impacts Galaxy Main, locals, cloud. Details: https://github.com/galaxyproject/galaxy/issues/2886
  10. Htseq-count Does not report standardized memory failure error message. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2532
  11. MAF tools Switching between data sources does not refresh tool form/dbkey list. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2828
  12. BWA-MEM default options produces BAM that fails ValidateSamFile. Default options for both. New ValidateSamFile tool likely needs tuning. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2846
  13. Fetch Alignments/Sequences Tool group. Toggle between sources does not refresh genome list on tool form. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2828
  14. Diffbind Produces green empty datasets with dependency issues. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2318
  15. MACS2 Callpeak Errors out but job produces result data (in red datasets). Impact Galaxy Main http://usegalaxy.org and possibly other installs. Details: https://github.com/galaxyproject/tools-iuc/issues/1033
  16. MACS2 CallPeak This tool has a current known issue with the option Fold Enrichment. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-iuc/issues/583
  17. MACS2 bdgdiff Produces green emtpy datasets for all output options . Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2226
  18. EBI SRA Tool errors when loading .bz2 compressed data from the "Submit files (galaxy) link. Details and workaround: https://github.com/galaxyproject/galaxy/issues/1709
  19. Trackster and BED datasets Fail to load with a specific error. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/1722
  20. Picard Tool: CollectRnaSeqMetrics Impacts Galaxy Main http://usegalaxy.org. Original Details: https://trello.com/c/XXlFa5ZL. Still fails with updated tool version 1.136.0. https://github.com/galaxyproject/galaxy/issues/1710.
  21. MEME Likely has dependency issues. Update on Main pending. Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/1913

Re-test to confirm correct at http://usegalaxy.org

Fix or enhancement, but not yet implemented at http://usegalaxy.org

  1. Needs main update (new repo https://github.com/galaxyproject/tools-iuc/pull/1005) Deep Tools correctGCBias Unrecognized arg --filterOut produces an error. Impacts Galaxy Main http://usegalaxy.org but is core tool issue. Details: https://github.com/fidelram/deepTools/issues/434
  2. Needs main update (new repo same as above) Deep Tools multiBamSummary Doesn't always produce output. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/fidelram/deepTools/issues/436
  3. PASS on Test, needs Main update Upload Problematically padding spaces to tabs when number of pasted columns varies. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2602
  4. Upload Is assigning "pileup" as autodetected datatype in a greedy way for tabular format data. Impacts Galaxy Test and Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3001

Recently corrected/implemented at http://usegalaxy.org

  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 http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2533
  2. Deeptools Fails for a specific error. Tool has been revised and pending upgrade. Impacts Galaxy Main http://usegalaxy.org. Details and link to work-around posted at Galaxy Biostars: https://github.com/galaxyproject/galaxy/issues/2331. Other issues with tool at Galaxy Main, perhaps global (see ticket) https://github.com/galaxyproject/tools-iuc/issues/835
  3. Convert Formats: Convert BAM to ScIdx Fails for dependency issue. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2460
  4. Group Fails under specific conditions. Fixed, pending deployment. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/pull/2166
  5. Multi-join Has dependencies issues. Impacts Galaxy Main http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/2511
  6. GenomeDiversity Admixture Dependency/config issue. Impacts Galaxy Main http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/2641
  7. BAMTools Convert, Merge, Randomize Fails for Convert to Bed + Yaml. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/378
  8. VCF-VCFintersect Needs to be updated in the Main Tool Shed and Galaxy Test/Main servers. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/391
  9. Bedtools SpacingBed Dependency/config issues. Impacts Galaxy Main http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/2640
  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 http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/365
  11. Duplicates in UI Display of Tabular Datasets Fixed, pending deployment. Impacts Galaxy Main http://usegalaxy.org and all other Galaxy flavors. Details: https://github.com/galaxyproject/galaxy/pull/2527
  12. Multi-join Frozen tool form options (related to icon display, see linked issues in ticket). Impacts Galaxy Main http://usegalaxy.com. Details: https://github.com/galaxyproject/galaxy/issues/2512
  13. Fetch Alignments/Sequences MAF tools have a dependency issue. Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2187
  14. Summary Statistics Fails for dependency issue. Impact http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2210
  15. CloudMap: "Hawaiian Variant Mapping with WGS" Dependency issues. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2304
  16. HISAT2 Fails, updating tool repo version on Main in progress. Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2246
  17. Tophat Execution with a single fastq file (unpaired) produces an error. Wrapper or dependency issue. Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2155
  18. Picard Tool: ValidateSamFile Errors (as a green successful dataset) in summary mode. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/369
  19. FastQC, MACS2 HTML results do not display when "eye" icon used. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2240
  20. Trim leading or trailing characters Fails when option to specify input is fastq is used. Impacts Galaxy Main http://usegalaxy.org and possibly locals running 16.04. Details and workaround: https://github.com/galaxyproject/galaxy/issues/2245
  21. CollectAlignmentSummaryMetrics Fixed on Main at version 1.136.0. https://github.com/galaxyproject/galaxy/issues/1692

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 http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2502
  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 http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2838
  3. Workflows Multiple input modifications within the editor triggers a browser crash. Impacts Galaxy Main http://usegalaxy.org (and potentially other Galaxy flavors). Details: https://github.com/galaxyproject/galaxy/issues/2835
  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: https://github.com/galaxyproject/galaxy/issues/1470

  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 http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/1132

  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: https://github.com/galaxyproject/galaxy/issues/1744

  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: https://status.galaxyproject.org/

  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. https://biostar.usegalaxy.org/