[release-testing-22.05] Tutorials with steps that are difficult/incompatible with Galaxy version 22.05

[cat-bro]

The 22.05 release testing team is running a set of GTN tutorials on usegalaxy.org running Galaxy 22.05. This issue is to keep track of issues that arise running the tutorials.

Galaxy 101

• Hands-on: Create history -> 2. Rename your history: detailed instructions for renaming the history do not fit with the new UI
• Hands-on: UCSC genome browser -> To visualize the data in UCSC genome browser, click on "display at UCSC main" option visible when you expand the history item.: The 'display at UCSC main' option for the final bed dataset is not available in the new history panel.

[hexylena]

We do not yet have a plan for the multi version instructions needed, let's add that to the @galaxyproject/wg-goats discussion today @shiltemann @Delphine-L

[hexylena]

And what happened to display at ucsc? Is t just gone?

[mvdbeek]

It's still there ? As before, you need to have a valid dbkey assigned, is that the case ?

[mvdbeek]

[cat-bro]

For the tutorial dataset (a bed file with db hg38) if I click on the Visualize button there are the options: 1. display in IGB; 2. display with IGV but not an option for the UCSC main genome browser. If I switch to the legacy history panel display at UCSC main is an option. It's the final dataset in this history https://usegalaxy.org/u/cat-bro/h/galaxy101

[ahmedhamidawan]

I've made comments on some of the tutorials that need to be updated, in this document: https://docs.google.com/document/d/1Ka5qedSnE2FQyb-uoXXBK7euaofVj03XshRfQX78ON0/edit Should those go here too? ( @jdavcs ?)

[cat-bro]

'Searching Your History' tutorial (1) Basic search instructions are not correct

Enter any text that a dataset you’d be looking for would contain, including:
- the name or part of the name  # this works
- any text (or partial text) from the info field. # this does not work
- the file format or reference database.  # this does not work
- any text or partial text from the annotation or tags of a dataset. # this does not work

Only the 'name' search works from the list above. This is probably not a bug since there is a new advanced search feature for searching by extension or tags

(2) Advanced search instructions are out of date. = needs to be replaced with : for terms like name=cactus (now name:cactus)

(3) Some of the advanced search terms do not work. name, hid, tag and state filtering works. format has been replaced with extension and this works database, annotation, info and history_content_type filtering does not work. The search terms covered in the tutorial do work with the legacy history [EDIT] the set of filtering options for the new history were introduced in this PR https://github.com/galaxyproject/galaxy/pull/13591

'Understanding Galaxy History system' also contains the search instructions above as well as very specific labelled pictures of history items and instructions on renaming the history panel that will need updating.

[ahmedhamidawan]

Extracting Workflows from Histories tutorial:

• [ ] Hands-on: Extract workflow: Gear icon (for history options) needs to be updated with the new history options icon
• [ ] Hands-on: Managing your histories: Table icon (for switch history) needs to be updated with the new switch history icon

Name tags for following complex histories tutorial:

• [ ] Note that non-name tags are now visible in the new history? ( Do not need to expand dataset to find non-name tags anymore )

Use Jupyter notebooks in Galaxy tutorial:

• [ ] Hands-on: Lauching a Jupyter notebook from the Visualize tab: Can't find Interactive Environments section under the Visualize tab (Same applies to Hands-on: Launching a Jupyter notebook from a dataset or a saved Jupyter notebook)

Multisample Analysis tutorial:

• [ ] Screenshots outdated
• [ ] Indicates Galaxy’s test server is ‘currently’ was being used at that time, so tutorial might need to be updated to the current release

[cumbof]

Rule Based Uploader: Advanced tutorial

• Hands-on: Build Collection from Uniprot Accession IDs Point 6 (JSON Rule Definitions): but before clicking “Build” must be replaced with but before clicking “Upload”, since it refers to the Build Rules for Uploading Datasets window;

• Hands-on: Build a matched collection Point 2: I uploaded multiple data and played with the Rules, but the history button near the wrench icon, as shown with the figure in this part of the tutorial, never showed up. Problem occurs on Chrome. Icon appears on Safari but it does not work #14175;

• Hands-on: Building Nested Lists Point 1: the first figure does not match with the tutorial. It says to paste a table but the figure shows a tabular data loaded from a History Dataset.

Galaxy 101 for everyone tutorial

• Hands-on: Converting dataset format Point 1 (Tip: Converting the file format): Click the Convert datatype button must be replaced with Click the Create Dataset button;

• Hands-on: Extract workflow Point 2: the gear icon must be replaced with the arrow icon, and of course the images must be also updated to match the new menu.

Group tags for complex experimental designs tutorial

• Hands-on: Set group tags during upload Point 1 (Tip: Creating a new history): is the If the new-history is missing: block still required? Point 6: after clicking on the Build button, the Galaxy Upload Manager window disappears #14154. Problem occurs on Chrome. It works as expected on Safari;

• Hands-on: Set group tags using the "Tag elements from file" tool Point 4: the Tag elements from file tool is now named Tag elements; Also, the resulting collection is named as ... (Tagged), but no tags are visible on the collection even if the collection has been correctly tagged;

• Hands-on: Running DESeq2 with group tags Point 1: the last step Output normalized counts table: Yes must be expanded to something like Under "Output options", select the "Output normalised counts" output selector.

A short introduction to Galaxy tutorial

• Hands-on: Name history Point 2: Click on the history name should be replaced with "Click on the pencil icon", and of course the figure must be updated;

• After the Hands-on: View the dataset content, the plural word bacteria should be replaced with bacterium;

• Hands-on: Extract workflow Point 2: the gear icon does not exist anymore and should be replaced with the arrow icon. Figure must be also updated;

• Hands-on: New history Point 1: does it make sense to keep the If the plus-sign is missing block? Point 2: Again, Click to rename history doesn't work anymore and should be replaced with something like Click on the pencil icon;

• Hands-on: View histories Point 1: the View all histories icon does not exist anymore and should be replaced with Show Histories Side-by-Side under the new history menu (arrow button).

NGS data logistics tutorial

• Hands-on: Creating a subset of data Point 9: In "List of fields" select Column: 1 must be replaced with something like Set "Cut columns" to c1;

• Hands-on: Running fastp Select paired collection(s): list_paired must be replaced with Select paired collection(s): Pair-end data (fasterq-dump);

• Hands-on: Map sequencing reads to reference genome The name of the BWA-MEM tool must be updated to Map with BWA; "Use the following dataset as the reference sequence": output must be updated with the the name of the GCF file in history GCF_009858895.2_ASM985889v3_genomic.fna.gz (as fasta); "Single or Paired-end reads": Paired Collection must be updated with Paired fastq collection;

• Hands-on: Remove duplicates output of Map with BWA-MEM must be updated with output of Map with BWA;

• Hands-on: Realign reads around indels "Reference": output (Input dataset) must be updated with the the name of the GCF file in history GCF_009858895.2_ASM985889v3_genomic.fna.gz (as fasta)

• Hands-on: Add indel qualities Again, "Reference": output (Input dataset) must be updated with the the name of the GCF file in history GCF_009858895.2_ASM985889v3_genomic.fna.gz (as fasta)

• Hands-on: Call variants One more time, "Reference": output (Input dataset) must be updated with the the name of the GCF file in history GCF_009858895.2_ASM985889v3_genomic.fna.gz (as fasta)

• Hands-on: Annotate variant effects There are two SnpEff eff tools. The tutorial should point the user to the SnpEff eff: annotate variants for SARS-CoV-2 tool; The last three points Annotation options, Filter output, and "Filter out specific Effects": No are set to their default values, so there is no need to keep them on the tutorial.

Whole transcriptome analysis of Arabidopsis thaliana tutorial

• Hands-on: Dataset subsampling The Sub-sample sequences files tool does not exist on usegalaxy.org