Question: Super Transcript Utility in Galaxy
0
gravatar for sdbaney
10 weeks ago by
sdbaney10
sdbaney10 wrote:

https://github.com/trinityrnaseq/trinityrnaseq/wiki/SuperTranscripts I read here that there is a utility within galaxy to allow me to assemble a SuperTranscript since I am working with RNAseq data from a non-model organism and no reference genome. I can't find any tools within galaxy to help me create this.

assembly trinity galaxy rna-seq • 149 views
ADD COMMENTlink modified 10 weeks ago by Jennifer Hillman Jackson25k • written 10 weeks ago by sdbaney10
1
gravatar for abretaud
10 weeks ago by
abretaud20
France
abretaud20 wrote:

It seems to be an easy galaxy tool to write. The best would be to add it at https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity No promise, but I'll try to do it if I find some time soon

ADD COMMENTlink written 10 weeks ago by abretaud20

Very nice, thank you!

ADD REPLYlink written 10 weeks ago by Jennifer Hillman Jackson25k
1

I've just opened a pull request there: https://github.com/galaxyproject/tools-iuc/pull/1937

ADD REPLYlink written 9 weeks ago by abretaud20
1

What is a pull request?

ADD REPLYlink written 9 weeks ago by sdbaney10

Changes made by an author against an existing repository are submitted as a "pull request" or "PR". In short, it is how a revision control system accepts, reviews, approves, and keeps track of changes.

Click on the link to see what was done and the status. I'll be linking in a tracking ticket for an update to https://usegalaxy.org once it looks ready to go, which you can then follow to find out when the tool is available at that server. Also, once the PR is approved, the updated tool suite (with the new wrapper) will also be in the ToolShed for use in a local/cloud/docker Galaxy.

Good question and hope that helps to explain how to interpret this info.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Jennifer Hillman Jackson25k

I went ahead and created the tracking ticket for Main. It is linked from the PR and also here: https://github.com/galaxyproject/usegalaxy-playbook/issues/143

ADD REPLYlink written 9 weeks ago by Jennifer Hillman Jackson25k

Hi Jen! I am trying to track this progress and see that it is currently ticketed with an update trinity once in main tool shed to capture the wrapper for this super transcript utility. Is this something I need to do? Or just keep searching for the utility? (thank you for all your help, I really appreciate it!)

ADD REPLYlink written 8 weeks ago by sdbaney10
0
gravatar for Jennifer Hillman Jackson
10 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This Trinity utility has not been wrapped for Galaxy in the ToolShed: https://usegalaxy.org/toolshed/

I would suggest trying the public Galaxy that the authors recommend. If it is not there, you could ask the tool authors if there are plans to wrapped/add this to a public Galaxy and/or wrap it in the ToolShed for use in your own local/cloud/docker Galaxy server. https://github.com/trinityrnaseq/trinityrnaseq/wiki/Accessing-Trinity-on-Publicly-Available-Compute-Resources

It may be that it is only available line command. Instructions are on the same wiki above and they can help with troubleshooting as needed.

I also asked the IUC developers if there are any plans for this in future development. Please follow or join in on the question at Gitter here: https://gitter.im/galaxy-iuc/iuc?at=5b19a05d106f3c24bde286e6

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Jennifer Hillman Jackson25k
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