Question: Can I execute multiple Trinity assemblies at once?
0
gravatar for rrodger
3 months ago by
rrodger0
rrodger0 wrote:

Hi all,

I would like to conduct many (~100) transcriptome assemblies using Trinity. I have been unable to find a way to script the process before on other clusters, and have had issues getting the full cleanup function to work. Is there a way to execute many transcriptome assemblies at once using Galaxy?

Thanks!

Rachel

trinity rna-seq • 132 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by rrodger0
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

Yes, multiple Trinity jobs can be launched at the same time with Galaxy. I am not sure if these will execute simultaneously or sequentially, but all least all can be started then you can come back for the results after.

Consider putting the analysis in a workflow. If run with a workflow, notifications can be sent after certain jobs or the entire workflow is completed (these are workflow options within the editor).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson22k
0
gravatar for rrodger
3 months ago by
rrodger0
rrodger0 wrote:

Hi Jen,

Thanks for the response! So there is a way for me to upload my 100 pairs of read files, and set up the workflow so Trinity can automatically select the correct input files without me interacting with it? How would I go about doing that?

Rachel

ADD COMMENTlink written 3 months ago by rrodger0
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