Question: Installing tool crossmap results in "frozen" state in local 17.05
gravatar for christopher.previti
7 months ago by
christopher.previti0 wrote:

Dear all, I have a rather strange issue with the tool shed installation monitor of our local Galaxy instance. One of the tools that I wanted to install is "frozen" in the "installation" state and can't be removed. I restarted Galaxy but it will not go away. Anybody have advise for me?

Cheers, Christopher Previti

ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson24k • written 7 months ago by christopher.previti0

Some more details would help:

  • Which Tool Shed was the tool sourced from?
  • If a public tool shed, what tool is problematic? (specifically - by link to the repo/version if possible)
  • And, what version of Galaxy are you using?
ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson24k

Hi, Yes of course, more information would be helpful: The tool was crossmap which I had to try because l was not able to get lift-over to run (other story):

Name: crossmap

Owner: yhoogstrate

Revision: 9c7cc3690f33

Installation Status: Installing tool dependencies -> this state is basically "frozen"

The toolshed was the Galaxy Main Tool Shed and we're running the latest Galaxy version.

Thanks again, Christopher

ADD REPLYlink written 7 months ago by christopher.previti0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson24k wrote:


Thanks, that does help. This tool was reported earlier as problematic:

No reports of a frozen install have come up before. I pointed the owner to this post and the other, so they may reply back here, but the usual process for reporting problems with tools not owned by devteam or iuc is to send a message through the Tool Shed's "Repository Actions > Contact the tool owner" function (log into the Tool Shed, search for the tool, click into it and find the menu in the upper right corner).

To get rid of it you could shut down Galaxy, edit the tool configuration files, and delete any associated tool installs/data files to remove all traces of it. This may be what the author suggests if the install is in a state that cannot be repaired with the usual method (uninstall). They should be able to provide you with the details.

If you need technical help for the liftOver tool (this should work in a default 17.05), you might try the mailing list. More server admins and developers will see the post, which is good if complex troubleshooting is needed.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson24k
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