Hi - this may be longwinded but I am somewhat new to this and would like to be as polite and helpful as possible.
I have been trying (to no avail) for a few days to run Galaxy using a local instance and despite scouring the web for similar problems, am unable to find a solution.
I installed the latest version of galaxy from git using the following [note: initially, I installed the galaxy packages outside my Anaconda3 folder but have since removed and reinstalled Galaxy in the proper Anaconda3 base path which contains the python and anaconda-navigator programs]:
$ git clone -b release_20.09 https://github.com/galaxyproject/galaxy.git
After installation, I changed directories to the galaxy folder within the anaconda3 directory and used:
$ sh run.sh
I get one of two types of “errors” —
{1} Either the program runs indefinitely (gets stuck on a step but does not return an error) and does not provide the local server link. Pasted below is the last message received when this happens.
[database_heartbeart_main.web.1.thread] main.web.1 is config watcher
galaxy.tools.search DEBUG 2021-01-24 15:42:16,103 [p:25634,w:1,m:0] [Thread-1] Toolbox index finished (42.075 ms)
{2} The other error happens if I kill this script/close the terminal while it’s running, and try to create another instance. I get a message stating “probably another instance of uWSGI is running on the same address” and “Address already in use”. To get around this I have been running the following, as it seemed to be a solution for others on the forums:
sudo pkill -f uwsgi -9
The next time I try to to create an instance, I get the first error (stuck). This cycle then continues (stuck → force quit → server in use → sudo kill → stuck)
Any help would be appreciated! I will be starting two courses soon - one on stem cell biology and one on machine learning for medicine, and I feel that understanding what’s going wrong with installation will help me troubleshoot future problems and actually being able to use the galaxy data management tools locally would be good. Please let me know if any further details are required.
[UPDATE]: I figured it out and/or it figured itself out. Keeping this here till I figure out how to mark as resolved or remove.