Hello all, I have just installed galaxy 24.1 in my local machine. Basic setup has been done (just setting up the admin user, download some tools) and some simple analysis can be successfully conducted.
However, when I tried to run Dorado, it immediately stopped with error. The error log showed:
“File /home/mk1b/galaxy/tool-data/sift_db.loc specified by the ‘filename’ attribute not found”
The file “sift_db.loc” does not exist but sift_db.loc.sample is there. Shall I just delete the “.sample” and save another file?
In addition, if I try to run some tools that require / can utilize GPU resources, shall I install CUDA container toolkits (for docker and/or other)?
Run run.sh stop to stop the Galaxy service.
In the Linux system, execute the command: cp sift_db.loc.sample sift_db.loc
Then, edit the sift_db.loc file with vim and modify or add the entries you need.
Finally, restart the Galaxy service by running run.sh start.
Many thanks Naibin, what would be the file “sift_db.loc” for ? Indeed, I have no idea what it is and how to modify it. would it be related to specific file loading / reading ? thank you.
Are you installing tools from the Main tool shed? As an example, this is the tool you mentioned, and it was just updated, so you’ll want to use the updated version Galaxy | Tool Shed
What is reported in your server logs?
Is there anything special about your server?
Let’s continue from there, thanks!
(All that said, yes, the advice from @Naibin_Duan is usually the way to go with a “missing loc” file – but in this case, that particular loc probably isn’t important. What it is for is described inside the file itself in the commented lines at the top, same as most loc files unless the tool README reports otherwise)
