Testing and tool/doc updates

[jennaj]

Move all of this into a Project

Note: click on labels to find all of a particular type in this repo. No tags for usage testing status (as installed/integrated on main) in the other repos, but comments are included below for test status. Not everything is captured -- this represents issues that users have reported or that were uncovered by general testing/usage. Issue order does not (usually) indicate priority/ranking.

Testing help is welcomed. Please don't check anything off unless you have actually tested it and linked tickets/PRs get closed. Many of these are bugs that only show up under specific conditions. We need to confirm those are resolved. Users follow these tickets, especially those that reported the bug to begin with.

If you help test on main/eu, you can use the test histories included in most issues to reproduce the problem and confirm fix/close ticket(s). Comment and ping @jennaj if you are not sure if the item should really be closed out or if you want a 2nd review. When testing (closed out or not), please include details: tool version, where tested (URL), alternative test history share link.. in the primary issue's comments and check it off as done in here if original problems fixed as installed on main/eu (not just a dev local).

Meta Active

• See if the latest MACS2 presents with this issue: https://docs.galaxyproject.org/en/master/admin/conda_faq.html#what-can-i-do-about-this-placehold-error. Example Q&A: https://biostar.usegalaxy.org/p/27086. IUC gitter abt same https://gitter.im/galaxy-iuc/iuc?at=5aa6d7db458cbde557279fe5
• Update/retest/ping everything still open at Known issues vs 18.01/18.05 https://galaxyproject.org/support/tool-issues/
• Retest/update tool updates listed here under issues plus add any still failed tests versus 18.05 for main/mirrors to known issues

Active

Main

• Saved Histories list -- options that don't work yet or could use tuning plus ok's Saved Histories list -- options that don't work yet or could use tuning plus ok's galaxy#5871
• "Peek view" scroll different between Chrome and Safari https://github.com/galaxyproject/galaxy/issues/6117
• Annotate with DGI Fix tool or remove from main? Annotate with DGI 0.1 - silent tool error  tools-devteam#504. https://github.com/galaxyproject/galaxy/projects/8#card-8100080
• CDT Fix tool or remove from main? CTD v 1.0.0 missing dependencies at http://usegalaxy.org galaxy#4303. https://github.com/galaxyproject/galaxy/projects/8#card-8100080
• Remove or tag deprecated tools GATK https://github.com/galaxyproject/galaxy/projects/8#card-7663074 & https://github.com/galaxyproject/galaxy/issues/3607 and Cloudmap https://github.com/galaxyproject/galaxy/projects/8#card-7663634 & Consider adding deprecated tag to all deprecated tools directly at http://usegalaxy.org galaxy#4183
• Related - mark Cuff tools on usegalaxy.org to align with usegalaxy.eu (deprecated)*?. https://github.com/galaxyproject/galaxy/projects/8#card-8100080
• Align other tools? Some or all?. https://github.com/galaxyproject/galaxy/projects/8#card-8100080

New BAM datatypes

• Re-test more new bam datatypes Do once tool produce/use these (qname_sorted.bam, qname_input_sorted.bam). Tests for new bam datatypes  #102

Tutorials

• Mothur GTN tutorial 5/29: ready to test against updated tools/datatypes. Summary of issues to have GTN 16S Mothur/Metagenomics tutorial usable on Main #74

VCF datasets/tools

• Test VCF Mani tools Older versions displayed from tool menu with no warning that a newer version if available. Some older versions buggy/shouldn't be used. Tool form banner alert "There is a newer version of this tool" for re-run jobs is not displaying anymore galaxy#3021 && VCF-VCFintersect needs to be updated in the Main Tool Shed and Galaxy Test/Main servers tools-devteam#391
• VCFFilter Needs the tool help updated to reflect the new form structure plus requested clearer error messages for commonly reported bugs (nearly all are malformed filter terms, we can catch those). VCFfilter (Galaxy Version 1.0.0_rc1+galaxy1) -- tool help is a mismatch versus the updated form query structure, impacts Coursera tutorials tools-iuc#1910

Upload && Get Data

• EBI SRA incorrectly assigns "fastqsanger" to "fastqsanger.gz" outputs. Also, if the data is really in "fastqcssanger.gz" format, it is assigned "fastqsanger" Get Data > EBI SRA is assigning fastqsanger to fastqsanger.gz output galaxy#6334
• Get Data tools meta change - Data Source Tool: Don't use output as config file Data Source Tool: Don't use output as config file galaxy#6245
• Upload duplicate dataset name problem Upload naming issues galaxy#6138
• CONVERTER_interval_to_bed_0 - fails during upload (when envoked) and when using Edit Attributes > Convert. CONVERTER_interval_to_bed_0 is crashing with latest bx-python version galaxy#6379

Datasets

• Dataset links - Old links to datasets no longer work. Example: datasets included in UCSC Sessions. New persistent links are planned for, but how older links if/will remain functional is TBD Ticket: provide persistent links to all shareable Galaxy objects provide persistent links to all shareable Galaxy objects galaxy#6645

Collections

• Collection download problems. @martenson creating new issue for problems with trying to download a collections using curl or wget #85 (comment) make sure linked and close out problems with trying to download a collections using curl or wget #85.
• Collection filters/functions test once implimented. Tickets Remove empty file from a dataset collection galaxy#5090 (empty datasets) & Improvements for Collection Operations galaxy#2496 (many enhancements)
• Retest deleted collection datasets Collections - deleting and purging problematic  galaxy#5402

Workflows

• Workflow extraction problems on main Tracking ticket for workflow extraction problems on main #109 links to Extracting a workflow from a history results in a failure #99
• Workflow extraction issues related to manually unhidden datasets and certain tools plus a bad GUI link: Extracting a workflow from a history results in a failure #99
• Deleting a workflow does not remove it from the Tool Panel (when pinned) Deleting a workflow does not remove it from the Tool Panel (when pinned) galaxy#5318
• Test Workflow Editor tool search box missing clear / closing X once fixed Workflow Editor tool search box missing clear / closing X galaxy#5671
• Retest workflow collection/Inputs problems after fixed: Workflow invocation fails when collections input is selected at runtime galaxy#5632
• Retest workflows version conflicts resulting in dropped input connections after fixed Improve display of queued versus hidden dataset counts on Saved Histories view galaxy#5554
• Retest workflow custom genome selection Is from 2015 - might be fixed already Workflow genome selection inconsistent with few bugs: fixed vs runtime galaxy#1132

Tools

• Retest Diffbind 2.6.6.4 Update Diffbind to version 2.6.6.2 (currently at 2.6.5.0) #127. 9/6/18 retest in progress
• Update Featurecounts once ready (usage fixes) Update Featurecounts once ready (usage fixes) #139
• Update RNA STAR 2.5.2b-0 database assignment fix, all outputs Update RNA STAR 2.5.2b-0 (database assignment fix) #134
• Related to RNA-star upgrade there is one common usage issue that might be addressed in the new version. Ticket to check/ask about tool form enhancement was created here: RNA STAR allows job submission when required inputs are missing, results in obscure cluster error tools-iuc#1777
• Mpileup will need an update once corrected and in MTS Mpileup will need an update once corrected and in MTS #133
• Circos graph problems. Tool needs fix then update on main. Ticketed Circos Builder (Galaxy Version 0.9-RC2) tool issue - pending fix, then update main to latest in MTS #105 (.org) and Circos 0.9-RC2 tool issues tools-iuc#1919 (iuc fix request)
• MAF tools errors: header only "green" empty datasets + python failures for simple queries. MAF tools errors: header only "green" empty datasets + python failures for simple queries #130
• Join two Datasets (Galaxy Version 2.1.1) -- incorrectly inherits 1st inputs datatype Join two Datasets (Galaxy Version 2.1.1) -- incorrectly inherits 1st input's datatype galaxy#6107
• MultiQC does not recognize raw data (txt) from FastQC when in a collection MultiQC does not recognize raw data (txt) from FastQC when in a collection #114
• MultiQC Version 1.2.0 does not include this yet but looks like it might in the next rev: Enhancement to filter inputs better (MultiQC should not accept HTML/graphics inputs - just text/tabular). As part of this, output more informative FastQC output datatype/dataset names to prevent users from choosing incorrect inputs. Details include followed up on 3/2/18: Update MultiQC to reject or report in error/help that HTML input is not valid tools-iuc#1538
• Check/Test if compressed inputs work with these tools, if now on main Update Fastq interlacer/de-interlacer + paired_end_joiner to fix bug with compressed inputs #67
• Freebayes in the tool panel twice (unassociated tool wrappers) Freebayes has both the updated and deprecated tool versions in the tool panel #108
• SnpEff Update/add sub-tools, fixes an important bug Update SnpEff tools to capture important bug fix (download) and new sub-tools  #157
• Test Cuffdiff update once on main. Update: v 2.2.1.5 SQLite option is a problem, prior version had the same problem but we fixed it server-side. Cuffdiff SQLite output problem #50 (comment)
• Enhance job errors for HISAT2 and Bowtie2. Will need main update ticket if/once done. Bowtie2: Improve datatype mismatch error detection, job failure, and bug report content tools-iuc#1789 && HISAT2: Improve datatype mismatch error detection, job failure, and bug report content tools-iuc#1790. @mvdbeek thinks this isn't need so we closed out. Watch bug reports going forward to see if this actually comes up for end-users. Update Might be opened again, mapping stats reports input problem but results are still green/success (BAM only contains the header) - plus rerun/switching tool versions (Bowtie 2.2.6.2 > 2.3.4.1) brings up hidden datasets as the default select. Different problem, may need a ticket: Bowtie2: Improve datatype mismatch error detection, job failure, and bug report content tools-iuc#1789 (comment)

FAQs

• Update Hub FAQs for FTP-loading and link to Troubleshooting to address actively transferring FTP loads listed in Upload/FTP staging GUI. Details: Upload displays FTP files while the the transfer is in progress - no warnings, can be imported as partial datasets #103 (comment)
• Update Hub FAQs to include this example for NCBI fasta download/upload. Biostars/graphics links in test history: https://usegalaxy.org/u/jen/h/test-history-ncbi-fasta-download-ftp-upload
• Update getgalaxy.org section for "how to become admin" with the yml config

General

• Galaxy start-up loops, known or fixed or wip? https://biostar.usegalaxy.org/p/27255/ and asked team here https://gitter.im/galaxyproject/committers?at=5ab5aa5bfa066c5325657e83
• Test Tools with optional output dataset directories fail if the directory does not exist once 18.01 updated on Main Tools with optional output dataset directories fail if the directory does not exist galaxy#5560
• Test Dynamically Generated Tool Parameters cannot be set until dataset has finished() once updated Dynamically Generated Tool Parameters cannot be set until dataset has finished() galaxy#3758

Enhancements

• Enhancement: Enable tag/anno edits for queued, executing, failed jobs Enhancement: Enable tag/anno edits for queued, executing, failed jobs galaxy#6330
• Wokflow share link view Modify GUI to offer links for "run, edit, save" and remove "import" when a shared workflow is already owned by the same user Modify GUI to offer link for "switch" and remove "import" when a shared workflow is already owned by the same user galaxy#6250
• History GUI ideas including dataset "map" view https://github.com/jennaj/support-known-issues/wiki/History-usability-ideas
• Workflows When a workflow is sent to a new history, that history link is not in the "launched" message anymore When a workflow is sent to a new history, that history link is not in the "launched" message anymore galaxy#6167. 6/18 Added bacl, update to main pending.
• Followup Active index selection on tools. Mapping tools Require an "active" database/genome index selection on tool forms galaxy#4499
• Tool version in UI: enhancement https://github.com/galaxyproject/galaxy/projects/8#card-7647616 & Make the latest Galaxy tool version or all versions available more accessible in the UI galaxy#5592
• GUI improvement ideas (some already done, some potentials for future) https://github.com/jennaj/support-known-issues/wiki/Enhancements

Other items

All here need follow-up/tickets: #94

[jennaj]

Priority -- tool updates 34a4dd4
update Main's tools

• remove all of anton's vcflib tools (were hidden). Older versions still present and the newest version is not what is chosen using the tool panel (known, fix in progress)
• remove all versions of vcffilter. One still on main (most current): VCFfilter: filter VCF data in a variety of attributes (Galaxy Version 1.0.0_rc1+galaxy1). Maybe meant "all old versions"? Related: https://biostar.usegalaxy.org/p/27277/
• update bamtools. Looks like only one tool updated: Filter BAM datasets on a variety of attributes (Galaxy Version 2.4.1).
• update Deseq2. v 2.11.40.1. Update Deseq2 to version 2.11.40.1 on main #101.
• update bowtie2. v 2.3.4.1. Update Bowtie2 from version 2.3.2.2 to 2.3.4.1 - includes important bug fixes #81. Runs great under most use cases. For reference, some minor items found re-testing a distinct issue for this tool (and HISAT2)-- "Enhance job errors for HISAT2 and Bowtie2" (listed above): Bowtie2: Improve datatype mismatch error detection, job failure, and bug report content tools-iuc#1789 (comment)
• update samtool_filter2. v 1.1.2. Samtools > Filter SAM or BAM Update Samtools Filter SAM or BAM - it fails to split on multiple regions and a fix has been made #78.
• update xy_plot. v 1.0.2. Graph/Display Data > Plotting tool Fix font problems in devteam/xy_plot tool #71.
• update sra_tools. NCBI SRA Tools >
  Download and Extract Reads in BAM & Download and Extract Reads in Fastq ; Download and Generate Pileup Format from NCBI SRA (Galaxy Version 2.8.1.2) ; Download and Extract Reads in FASTA/Q format from NCBI SRA (Galaxy Version 2.8.1.3). Update: For all three tools, extracting single accessions works (most of the time), but fails with multiple. Not sure if tool or server issue. Details in upgrade ticket: Update SRA tools: NCBI Download and Extract Reads in BAM + Fastq to version 2.8.1.3 #68
• update fastq_paired_end. Just this tool or all? Fastq interlacer v 1.2.0.1 de-interlacer v 1.1.2 + paired_end_joiner v 2.0.1.1 Update Fastq interlacer/de-interlacer + paired_end_joiner to fix bug with compressed inputs #67.
• install star_fusion
• update stringtie. v 1.3.3.1. StringTie transcript assembly and quantification Update Stringtie tools to new version #60. Also checking StringTie Merge v 1.3.3
• update featurecounts. v 1.6.0.3. Update featurecounts from on main once in Tool Shed #52.
• update bwa. BWA-MEM also updated. BWA v 0.7.17.4 -- BWA-MEM v 0.7.17.1. Update BWA and BWA-MEM on main #106.

Not in the list -- maybe the update was for bedtools and not bamtools (above)

• BedTools > Update to *NucBed 2.27.0.1 to capture a bug fix Update to NucBed 2.27.0.1 to capture a bug fix #83

[jennaj]

See the project instead https://github.com/galaxyproject/usegalaxy-playbook/projects/1