Error on: CFSAN SNP Pipeline

[Jane]

Dear Sir/Madam,

I met a error report as the following those are marked in yellow, when I run the workflow "CFSAN SNP Pipeline w/ Assembly Lite ", the link is “https://galaxytrakr.org/published/workflow?id=3eea0e5531b053f5”

Workflow cannot be executed. Please resolve the following issue:

Following tools missing: toolrepo.galaxytrakr.org/repos/jpayne/quast_select/quast-select/0.1.0, toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/map_reads/1.0.1, toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/call_sites/1.0.1, toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/filter_regions/1.0.1, toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/merge_sites/1.0.1, toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/call_consensus/1.0.1, toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/merge_vcfs/1.0.1, toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/snp_matrix/1.0.1

Would you please help me to resolve this problem?

[jennaj]

Hi @Jane

Thanks for sharing all of the linked data for context, very helpful!

Review

Messages like these are sometimes expected, and just mean that a tool included in the workflow is not available at the server where the workflow is being run.

@Jane

Workflow cannot be executed. Please resolve the following issue:

Following tools missing:

For you case there are quite a few! So looking into why is what to look at next.

The top level report for this workflow reports that it hasn’t been updated for about 6 years – since 2019!

What to do

Sometimes a server will host a different version of the same tool and the workflow editing program automatically updates the workflow but that doesn’t seem to be possible for these tools.

I checked the Galaxy ToolShed to investigate why. It seems that the tools were renamed. This makes the direct same-tool-different-version update process not possible. Instead, each tool will need to be replaced in the workflow and connected up.

I suspect that the tool forms and parameter organization has changed in ways that should be reviewed closely. So, be sure to check all of the options, especially the default parameters. The first tool that is connected but with some red areas indicates that the tool itself is available but some of the parameters changed enough to still need an adjustment.

Workflow Editing

Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy...

With more at → GTN Materials Search (query=workflow)

Workflow updates usually go something like this:

1. Disconnect all the noodles between tools.
2. Replace each tool with the updated/current version.
3. Decide on the inputs – will this be a collection input?
4. Set parameters for each tool.
5. Connect noodles between tools in the order of tool execution.
6. Review the Best Practices suggestions.
7. Test and revise until working.

The User Guide on the server likely also needs an update since it references this older workflow. Are you the one working on this? Or, do you want to help them to work on this? If yes, write into their mailing list linked on the homepage – we can help with general Galaxy usage at this forum but server tasks involve coordination with the local administrators.

Or, if this is just for yourself, you don’t need to coordinate! Anyone can create and modify their own copies of workflows, and then later publish them on the server.

Let’s start there, thanks!