Running galaxy stuck with "Activating virtualenv at .venv Updating service Gunicorn"

usegalaxy.org support
1

Hi,

I am new to Galaxy. And I am learning how to use the tool by following the tutorial. After I executed the command “./run.sh”, the tool started up but got stuck with “Activating virtualenv at .venv Updating service gunicorn”.

Not sure how long I have to wait till the updating end. May I know how to fix this problem? If it’s really a problem or just I need to be more patient. Thank you.

2

Are you sure the server is not running already?
Try to check 127.0.0.1:8080 (or whatever address you may have configured in your browser.

3

Hi, unfortunately, no. I tried almost all possible addresses, but none of them worked. Actually, I noticed this error when I re-run the ./run.sh
AttributeError: module ‘pysam.libcalignedsegment’ has no attribute ‘CMATCH’

4

Hi @Li_Ma

Do you still need help? If yes, could you clarify a few things so we can help you to solve this?

  1. Which tutorial please – the URL is the best way to designate it
  2. Are you developing a new tool? Are you using Planemo yet? Are you running in a development deployment of Galaxy?
  3. Or, are you starting up a new server to use for something else?
  4. Version of Galaxy you checked out from Github (and please describe if other).
  5. Are you running all of this from inside of a container?

Off hand, getting rid of the current venv (delete it entirely) and letting it be created again is one common solution whenever the initial run.sh doesn’t start up. So maybe try that first. Then you can share you new logs along with the information above.

If you did solve this great! Let us know! Or we can follow up to help. I’m linking some resources below for context. And know that if this server is just for you own use or a small group, the Docker version is so much easier to get started with the first time. :slight_smile:

XREf