Question: rgrnastar toolshed repo (RNA STAR) not configured properly in a local Galaxy - help
1
gravatar for starr34
3 months ago by
starr3420
starr3420 wrote:

I tried to install a new tool to my Galaxy instance from a toolshed toolshed.g2.bx.psu.edu): tool is rgrnastar (owner: iuc); (revision:d681e989ac95). When I go to "manage installed tool shed repositories" the status for this tool says "installed" however the tool never showed up in my tool list. I emailed in to the help desk for the Galaxy I use and they said that the toolshed repo may not be configured properly. They suggested posting on here. Any help on this would be much appreciated or an alternative tool for STAR that I can install.

rna-seq tool galaxy rnastar • 174 views
ADD COMMENTlink written 3 months ago by starr3420

The tool might have been installed as nested within a tool section left at default or accidentally specified to be not where you are expecting it. Try finding it by using the search function at the top of the tool panel and let us know if that works or not. The search term could be "rnastar" or "rgrnastar".

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson23k

I tried that already. I had set it to be put under NGS:RNA Analysis. I searched under this category and also performed a search once I couldn't find it there.

ADD REPLYlink written 3 months ago by starr3420
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

I would try uninstalling and reinstalling again. If that does resolve the problem, troubleshoot by:

  • Check your ./config/tool_conf.xml file - the tool should be populated there or it will not appear in the tool panel.
  • Upgrading to the most current stable Galaxy release 17_05 (if it is not in use). The newer versions of tools are designed to work best with this release (dependencies are handled differently with Conda).
  • Test install another tool that has been recently updated to see how that works. HISAT2 is one choice (another RNA-seq alignment tool).

Let us know how that goes and we can follow up from there. There are no known issues with the RNASTAR repository. The Tool Shed did recently undergo some changes, so I'll test install this repo as well.

https://docs.galaxyproject.org/en/master/releases/17.05_announce.html

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson23k

The uninstall/re-install did not work. I am unsure how to tell which Galaxy version I am currently using. It is the newest AMI that has been put out for that Galaxy but its possible its an old version since I just learned today that they can't easily update it. I'll try using the public galaxy for this program. Thank you for your help.

ADD REPLYlink written 3 months ago by starr3420
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