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BaobabLims / baobab.lims

Baobab LIMS is an open-source laboratory information management system (LIMS)
http://baobablims.org/
GNU General Public License v3.0
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Update docker-compose.yml #146

Closed shaze closed 2 years ago

shaze commented 3 years ago

Made the baobab volume absolute

When I ran docker-compose on I got this error

ERROR: for baobab_lims  Cannot start service baobab_lims: failed to create shim: OCI runtime create failed: invalid mount {Destination:baobab Type:bind Source:/var/lib/docker/volumes/f2f0b1b70754364ff9766d97c4ec9af37616d80a361628f41632743a827c097f/_data Options:[rbind]}: mount destination baobab not absolute: unknown

And an inspect of the resulting container shows that the dest

 "Mounts": [
            {
                "Type": "volume",
                "Name": "f2f0b1b70754364ff9766d97c4ec9af37616d80a361628f41632743a827c097f",
                "Source": "/var/lib/docker/volumes/f2f0b1b70754364ff9766d97c4ec9af37616d80a361628f41632743a827c097f/_data",
                "Destination": "baobab",
                "Driver": "local",

Doing some googling shows that the recommended solution was to change the destination to an absolute address and that worked flawlessly for me. There may have been some docker changes.

pvanheus commented 3 years ago

I think we need to investigate the error a bit more - having an absolute path in the Docker lib directory doesn't seem right. Also we are currently using a version 2.4 docker-compose.yml file - we should upgrade to a more recent version.

shaze commented 3 years ago

Maybe the problem then is our side as we are using docker-compose version 1.25. This is the standard Ubuntu 20.04 docker-compose installation candidate.

We're up and running so there's no need for action as far as we're concerned.