running any analysis from HistomicsUI fails at the end with a file permission problem. For exmaple color deconvolution:
Performing color deconvolution
Outputting individual stain images
/mnt/girder_worker/0f8cf5bbae6c4c28ac14e148844edfb2/Color Deconvolution-outputStainImageFile_1.png
/mnt/girder_worker/0f8cf5bbae6c4c28ac14e148844edfb2/Color Deconvolution-outputStainImageFile_2.png
/mnt/girder_worker/0f8cf5bbae6c4c28ac14e148844edfb2/Color Deconvolution-outputStainImageFile_3.png
[2022-04-30 13:19:16,261] ERROR: Error setting perms on docker volumes [‘/tmp/girder_worker/tmpfqc28zee’].
Traceback (most recent call last):
followed by a large number of errors. The analysis output in HistomicsUI is OK. Where can I set the permissions?
Best regards,
Kai
It looks like you are using the deploy_docker.py script to configure things. By default, the grider worker tries to write to /tmp/girder_worker from within worker volumes. My guess is that directory somehow has the wrong permissions. You can either specify a different girder worker temp directory with the --worker-tmp-root command line flag or ensure that that directory is writable by the appropriate user – I think this is the user that ran deploy_docker.py, but you could be certain by making it world writable (chmod a+rw /tmp/girder_worker).
– David
I have tried even with chmod -R but every new analysis run makes a new tmp directory with wrong permissions and the run fails at the end:
total 32
drwxrwxrwx 8 root root 4096 Mai 3 07:25 ./
drwxrwxrwt 14 root root 4096 Mai 3 06:47 …/
drwxrw-rw- 2 kai kai 4096 Apr 30 13:01 pymp-igl6phg6/
drwxrw-rw- 2 kai kai 4096 Apr 30 13:06 tmp_bmntw79/
drwxrw-rw- 2 kai kai 4096 Apr 30 13:18 tmpfqc28zee/
drwx------ 2 kai kai 4096 Mai 3 07:25 tmpgzowngto/
drwxrw-rw- 2 kai kai 4096 Mai 3 07:20 tmpo_dvc8iw/
drwxrw-rw- 2 kai kai 4096 Mai 3 07:22 tmpoj01wp__/
here nuclei detection fails on tmpgzowngto