Thanks!
ah, I think I found the docs for this: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-stdio
@cganote /var/log/syslog should be there.
Not seeing it:
root@eb13f41ba429:/var/log# ls
alternatives.log condor fsck proftpd upstart
apt dmesg lastlog rabbitmq wtmp
autofs.log dpkg.log munge slurm-llnl
bootstrap.log faillog nginx supervisor
btmp fontconfig.log postgresql unattended-upgrades
root@eb13f41ba429:/var/log# ls
alternatives.log condor fsck proftpd upstart
apt dmesg lastlog rabbitmq wtmp
autofs.log dpkg.log munge slurm-llnl
bootstrap.log faillog nginx supervisor
btmp fontconfig.log postgresql unattended-upgrades
Are you running slurm, htcondor or anything fancy like k8s?
or SGE?
watching with top, looks like it gets down to 500mb or so of available memory, so I'm guessing that's the issue
just wanted to confirm and see if the kernel kills it
Is it the docker that dies or just the job?
I had issues with the Docker dying. Accepted answer here is useful https://stackoverflow.com/questions/38112968/how-to-know-the-reason-why-a-docker-container-exits
I came really close to having submission through Workflow Execution Service (WES) with CWL working on the Arvados server. The test CWL runs with a lot of green but gets canceled before finishing: https://workbench.qr1hi.arvadosapi.com/container_requests/qr1hi-xvhdp-a21z0nwgwqmfblw
I need to debug what is going on, but glad to be making some progress. Thanks everyone for the motivation to work on these today.
the QIIME 2 visualizations have their own assets but they aren't known ahead of time
tracking issue: qiime2/q2galaxy#5
maybe @jxtx does not about it as well
However, there is a practical reason we are in favor of static assets, Galaxy is used in environments without internet connection.
is there any way to bundle this or all possible things in advance?
@ebolyen btw. great to "see" you again!
@bgruening ditto! The assets are still static, they just aren't known if that makes sense... The .qzv files are zip files with a /data/ directory (the visualization itself). So none of this requires internet (in fact we expect these visualizations to be entirely self-contained), but it does require "mounting" the data directory at some http-servable path
so ideally the visualization would get the HDA id and extract the .qza file to some temporary location and route some visualization-plugin specific prefix to that location
I will try to get a Vis expert and point him/her in your direction :)
oh, but it could return the "path", then the problem is just serving that path
galaxy tour is in preparation :)
Hi @/all, the next training CoFest of the Galaxy Training Network will be in one month, on the 15th of November: galaxyproject/training-material#1082
We plan to focus on genome annotation training; but anyone who would like to contribute on any other topics is very welcome to join.
We will coordinate via Hangout (drop-in channel we will keep open the whole day) and the GTN Gitter channel.
We plan to focus on genome annotation training; but anyone who would like to contribute on any other topics is very welcome to join.
We will coordinate via Hangout (drop-in channel we will keep open the whole day) and the GTN Gitter channel.
Hi @/all, the next training CoFest of the Galaxy Training Network will be in one month, on the 21st of February: galaxyproject/training-material#1152
Anyone who would like to contribute on any topics is very welcome to join.
We will coordinate via the GTN Gitter channel
During the day, we will also have a call meeting with the GTN to discuss the recent changes and future directions galaxyproject/training-material#1151
Anyone who would like to contribute on any topics is very welcome to join.
We will coordinate via the GTN Gitter channel
During the day, we will also have a call meeting with the GTN to discuss the recent changes and future directions galaxyproject/training-material#1151