Last updated 6-6-17

Current tool improvements and updates

Review of tools at http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-iuc/issues/1292

Issue by tool name

  1. (many) StringTie 1.3.3. Errors when output for DEseq2/EdgeR is selected. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-iuc/issues/1322
  2. (15) Heatmap 1.0.0 Missing dependencies. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3030
  3. (2 bugs +github) CummeRbund 1.0.1 Select for "gene_id" problematic. Graphs for Heatmap and Volcano plots also problematic. Impacts Galaxy Main http://usegalaxy.org.Details: https://github.com/galaxyproject/tools-devteam/issues/340
  4. (2) Du Novo: Align families 0.7 Tool updates removed the cluster targetting for Jetstream. Jobs are failing again for walltime. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3057
  5. (2) Freebayes 0.4.1 Now requires upsteam inputs have database metadata assigned. Even when a genome is selected within the workflow editor. This breaks some older workflows and published tutorials. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/409
  6. (1) SnpEff Download v4.1.0. Index problem for certain databases nested in .zip archives from the source. A newer version of all SnpEff tools is available (4.3k.0). Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-iuc/issues/1354
  7. (1) Annovar 0.2 Wrapper problems. Use v 0.1 as a workaround. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/4001
  8. (1) Picard SamToFastq 1.136.0 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
  9. 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: https://github.com/galaxyproject/galaxy/issues/2886
  10. (many) Htseq-count 0.6.1galaxy3 Does not report standardized memory failure error message. Suggested improvements are in the ticket. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2532
  11. Needs RE-TEST (many) MAF tools 1.0.1 Switching between MAF 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 0.7.12.1 produces BAM that fails ValidateSamFile 1.136.0. Default options for both. ValidateSamFile tool needs tuning? Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2846
  13. (many) Upload v 17.05 Retested 6/1/17 on Main. Still 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

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

  1. Trinity Both trinity and trinity_pcs. Details: https://github.com/galaxyproject/tools-iuc/issues/1298

Fixed pending update

Integration test once installed


Integration test

Retest/status update at Main and default 17.05

TOOLS

  1. Uniprot Dependency fix on 5/15/17. Impacted Galaxy Main http://usegalaxy.org, locals, cloud (any install). Details: https://github.com/galaxyproject/galaxy/issues/3721
  2. 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
  3. (21) MEME 4.11.1.0 Has dependency issues. Updates have not resolved usage problems yet (tool has never worked). Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/1913
  4. Stringtie (recently updated to 1.3.3). UI/version issues - needs ticket if not fixed in next day or so.
  5. MACS2 (recently updated to 2.1.1.20160309.0). Test all components against open issues above (two are confirmed to be problematic so far)
  6. Some parts fixed, some pending, see ticket. (30+ for all) 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 issues appear to be localized to the roundup cluster (default). Impacts Galaxy Main http://usegalaxy.org. https://github.com/galaxyproject/galaxy/issues/3556

UI

  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. 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
  3. 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

Issue by user interface behavior

  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: https://github.com/galaxyproject/galaxy/issues/1744
  2. 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

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: https://status.galaxyproject.org/
  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. https://biostar.usegalaxy.org/

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. GenomeDiversity PrepareInput gd_prepare_population_structure 1.1.0 Dependency/config issue resolved 1.2.0. Impacts Galaxy Main http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/4108
  2. DEXseq 1.20.1 Dependencies issues. Related tool DEXSeq Counts 1.20.1 already has fixed dependency issue. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3709
  3. MACS2 bdgdiff + bdgbroadcall 2.1.1.20160309.0 Tool version updated 4/11/17 errors with "macs2 command not found". Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2226
  4. MACS2 bdgdiff 2.1.0.20151222.0 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: https://github.com/galaxyproject/galaxy/issues/3925
  5. Cuffmerge v 2.2.1 Older v 0.0.6 is successful with same inputs. Closed unless reported again. 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
  6. 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 http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3709
  7. Deseq2 2.11.38 MTS update to 2.11.39 fixes dependency issues. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/4046
  8. Deprecated tool Draw phylogeny 1.0.0 Version 1.0.0 has a dependency issue. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3158
  9. Diffbind 2.2.0/2.1.0 Dependency problems fixed in 2.2.0 Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2318
  10. 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 http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3660
  11. 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
  12. Deep Tools multiBamSummary Doesn't always produce output. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/fidelram/deepTools/issues/436
  13. Tophat Tool is being deprecated and no longer runs on Jetstream (where original metadata problem was from). Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2838
  14. MAF tools 1.0.1 Fix made for legacy env updates. Extract Pairwise MAF blocks 1.0.1 https://github.com/galaxyproject/galaxy/issues/3934. GeneBed_Maf_Fasta2. (https://github.com/galaxyproject/galaxy/pull/3931). Tool Extract Pairwise MAF blocks may also need fix. Impacts Galaxy Main http://usegalaxy.org, locals, cloud.
  15. Trimmomatic Update to version 0.36.3 corrected tool form option "Illumina Clip" failures. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3691
  16. Picard Tool: CollectRnaSeqMetrics 1.136.0 Impacts Galaxy Main http://usegalaxy.org. Original Details: https://trello.com/c/XXlFa5ZL. 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. https://github.com/galaxyproject/galaxy/issues/1710.
  17. 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 http://usegalaxy.org. Details: https://github.com/galaxyproject/tools-devteam/issues/401
  18. Trackster and GFF/GTF datasets Fail to load with a specific error. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/3499
  19. EBI SRA Main 1.0.1 Tool errors when loading .bz2 compressed data from the "Submit files (galaxy)" link. Details and workaround: https://github.com/galaxyproject/galaxy/issues/1709
  20. 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
  21. 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
  22. DESEQ2 2.1.8.3 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. Convert Formats: Convert BAM to ScIdx Fails for dependency issue. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2460
  28. Group Fails under specific conditions. Fixed, pending deployment. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/pull/2166
  29. Multi-join Has dependencies issues. Impacts Galaxy Main http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/2511
  30. 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 http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/2641
  31. 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
  32. 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
  33. Bedtools SpacingBed Dependency/config issues. Impacts Galaxy Main http://usegalaxy.org. Details https://github.com/galaxyproject/galaxy/issues/2640
  34. 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
  35. 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
  36. 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
  37. Fetch Alignments/Sequences MAF tools have a dependency issue. Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2187
  38. Summary Statistics Fails for dependency issue. Impact http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2210
  39. CloudMap: "Hawaiian Variant Mapping with WGS" Dependency issues. Impacts Galaxy Main http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2304
  40. HISAT2 Fails, updating tool repo version on Main in progress. Impacts http://usegalaxy.org. Details: https://github.com/galaxyproject/galaxy/issues/2246
  41. 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
  42. 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
  43. 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
  44. 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
  45. CollectAlignmentSummaryMetrics Fixed on Main at version 1.136.0. https://github.com/galaxyproject/galaxy/issues/1692