search

usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
0 stars 0 forks source link

Tools issues week 3, 2023 #86

Closed tothuhien closed 1 year ago

tothuhien commented 1 year ago

There're a few tools that ended up with error. export_remote: the error message indicated "time out", so it seems to be not a tool's problem kraken_taxonomy_report: due to wrong input format from user's data report2gest: looks like wrong user's data format, but to look more in to details since this tool has never been run successfully

basic_illumination: there was a bug but was fixed by Kjetil. However, after that, some jobs ended up randomly with error status and message "Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock." even that the job seems to be done. Maybe something to be fixed with JAVA_HOME variable.

kjetilkl commented 1 year ago

I have already checked the JAVA_HOME variable, and it seems to be set correctly in the container. I am not sure if the error is serious, since STDOUT indicates that the tool completed successfully anyway. The error is related to persistance of Preferences, but I don't think this is necessary, and the error could perhaps be ignored in this context. However, the tool wrapper complains anyway since it uses an "aggressive error detection" strategy which triggers when the word "Exception" is found in STDERR.

I have conferred with the end user, and we have agreed to simply modify the wrapper to make it more admissive.

tothuhien commented 1 year ago

Thanks Kjetil, so I think I can close this issue here(?)