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.
I would try uninstalling and reinstalling again. If that does resolve the problem, troubleshoot by:
- Check your
./config/tool_conf.xmlfile - 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.
Thanks, Jen, Galaxy team