how it works in theory is that it takes the input dataset (which is a zipped-up neo4j data directory) and it unpacks it inside the container... thus all the unzip & stuff.
I think that error is happening because of the
"USER_GID" 2345 type config
I recall this container had to some how map a user on the host to a user in the container...
and it is commented in addition
it is commented in the command because it is in the
<environment_variables> block
And one general quesiton, Peter: all commands in the command block in GXiTs are commands executed WITHIN the containers, aren't they?
and yes, those are run in the containers
(venv) [galaxy@galaxy-hepp ~]$ node --version
v12.16.3
Any idea why images might not be pulled?
It works for ethercacl
I see the neo4j IE is mentioned in some issues - galaxyproject/galaxy#8899 and galaxyproject/galaxy#4145 - rather old issues. Sorry, this needs work :(
Hi, I am trying to make interactive tools working but I'm stuck at this error once I launch a tool:
galaxy.managers.interactivetool DEBUG 2021-05-20 12:22:51,832 [pN:main.job-handlers.2,p:26315,w:0,m:2,tN:LocalRunner.work_thread-0] Error removing entry (DELETE FROM gxitproxy WHERE key=? and key_type=?): no such table: gxitproxyI noticed, that the interactivetools_map.sqlite file has size 0 and doesn't actually contain anything. I'm using the usegalaxy_eu.gie_proxy role to install it. I'd be glad if anyone could point me out to the right direction.
18 replies
@hexylena:matrix.org Hi, I am trying the jupyter notebook after ethercalc. For ethercalc it will wait until the image is pulled and then start. For jupyter notebook it throws the error
/storage/galaxy/jobs_directory/000/117/tool_script.sh: line 9: jupyter: command not found almost immediately. Shall it not wait for the 6.65 GB image to get pulled?
4 replies
Does someone run a non-biology-centric Galaxy server that has been modified to actually strip away some or all of the bio-related UI content? Would you be willing to help this person? I don't know of any specific technical documentation around this -- but maybe there is a publication or ?? https://help.galaxyproject.org/t/remove-menu-for-genome-set-in-data-upload/5988
4 replies
so nothing is responding on the 8000 port inside container
could be, but 90% of the time it's on the systems/configuration side, the containers usually just work
fs.js:549
return binding.open(pathModule._makeLong(path), stringToFlags(flags), mode);
^
Error: EACCES: permission denied, open '/root/.forever/KkGt.log'
at Error (native)
at Object.fs.openSync (fs.js:549:18)
at Object.forever.startDaemon (/usr/local/lib/node_modules/forever/lib/forever.js:460:14)
at /usr/local/lib/node_modules/forever/lib/forever/cli.js:319:15
at /usr/local/lib/node_modules/forever/lib/forever/cli.js:162:5
at /usr/local/lib/node_modules/forever/lib/forever.js:412:11
at FSReqWrap.oncomplete (fs.js:82:15)
hard to say what causes what though :/
manually executing
forever start ethercalc --cors inside the container yields the same error
We might be the 10%.
does /root/.forever exist?
running the container with sudo
yeah,
<param id="docker_sudo_cmd">/usr/bin/sudo -u galaxy</param>
who is the user
i.e. if you
docker exec (when you say manually starting forever)
you sure? https://github.com/shiltemann/ethercalc-galaxy-ie/blob/master/Dockerfile#L5 makes it look like it should be root?
i don't see another USER statement dropping privs
$ whoami
whoami: cannot find name for user ID 1001
$ ls /root
ls: cannot open directory '/root': Permission denied
the job destination runs with the docker_sudo_cmd above, I suspect that is galaxy's id
docker_sudo_cmd should really only be for the command to run to be able to do
sudo docker run <container> which shouldn't affect the container