Question: Inaccessible workflows at CloudMap
0
gravatar for kamila.delaney
4 months ago by
kamila.delaney0 wrote:

Dear All!

I am trying to use the workflows available at CloudMap https://usegalaxy.org/u/gm2123/p/cloudmap, but every single workflow on this page after clicking on it shows me the internal error and is impossible to run. I just received my data and really wanted to use one of the workflows for my analysis, but the error persists for several days now and I am not sure what to do or whom to contact.
Did anyone encounter problem like this in the past and could share any advice with me? I would greatly appreciate that!

Thank you! Kamila

software error • 130 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson23k • written 4 months ago by kamila.delaney0
0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The Cloudmap pipeline at http://usegalaxy.org has been deprecated. There will be no more tool updates.

The Cloudmap Page is owned by the tool authors, hasn't been updated in a while, and I suspect that the links are no longer working correctly (producing the error). I was able to directly import a few of the workflows (as a test) by going under "Shared Data > Shared Workflows" and searching with the keyword "cloudmap". Perhaps try that route? Please be aware that you may encounter tool errors even if the workflow imports and jobs are started (several have been reported the last year or so). Tool errors for deprecated tools do not need to be reported further as there will not be any actions/changes to resolve them (here or via bug reports).

Your alternative is to set up a local Galaxy based on a Galaxy release version dated from around the same time that the Cloudmap pipeline was created. Import the tools from the Tool Shed and download/upload the workflows for use. How successful this will be is not a known, however, I can let you know that using the more recent versions of Galaxy will likely trigger tool/workflow errors in ways similar to how they currently fail at http://usegalaxy.org.

You could also ask the pipeline authors for advice (which version of Galaxy is known to still work with the workflow/tools, special configuration, and the like). Contact information on the Cloudmap page is still correct as far as I know.

Hope this helps to make a decision on how to proceed! Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson23k
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