Exporting workflow from tool shed respository

Question: Exporting workflow from tool shed respository

6 weeks ago by

llp • 0

llp • 0 wrote:

I'm trying to import a workflow from a galaxy tool shed repository, but when I go to workflow --> import --> archived work flow url and input the url (below) I get the message "The data content does not appear to be a valid workflow."

The workflow I am attempting to import can be found at the following url: http://toolshed.g2.bx.psu.edu/view/galaxyp/proteomics_rnaseq_sap_db_workflow

I'm new to galaxy and would really appreciate any advice on how to get this to work.

rna-seq galaxy • 93 views

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modified 5 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 6 weeks ago by llp • 0

5 weeks ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is an older repository with some custom tools, so it might not work under newer Galaxy versions. But you can try, or you can use more current workflows (an easier choice).

If this is your own Galaxy server, first try installing the repository.

If working at some public Galaxy, or one where you are not an administrator, the zip archive of the repository can be downloaded from the ToolShed, uncompressed, and the .ga workflow(s) directly uploaded. Most public Galaxy servers have newer versions of the included tools so some editing to get these to work will be needed (switch to updated tool versions, swap out tools when the original from the workflow is not installed/available at any revision).

For public Galaxy servers, the highest chance of success would be to use the GalaxyP public server. These workflows might be already available under Published Workflows, meaning, no need to re-upload workflows or install tools to test-drive the workflow before deciding to include it on your Galaxy.

If installing or running the workflow presents with errors (at GalaxyP or in your own Galaxy), you could ask the authors if these are still supported or not, or what replacements, if any, are available. http://galaxyp.org/ >> http://galaxyp.org/access-galaxy-p/

For current Galaxy tutorials and associated workflows, please see those hosted by the Galaxy Training Network >> Proteomics. There is a pre-configured Docker Galaxy available and the Public servers where these are known to work are listed under "Galaxy instances".

https://galaxyproject.org/learn/ >> https://galaxyproject.github.io/training-material/topics/proteomics/

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 5 weeks ago • written 5 weeks ago by Jennifer Hillman Jackson ♦ 25k

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