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    Björn Grüning
    @bgruening
    Thanks!
    Brad Chapman
    @chapmanb
    Thanks for the pointer, done: galaxyproject/training-material#965
    Björn Grüning
    @bgruening
    Thanks!
    Carrie
    @cganote
    Anyone happen to know where system messages are being printed in docker-galaxy-stable? No /var/log/syslog, messages, secure, etc; I suspect one of my jobs is being oom-killed.
    Björn Grüning
    @bgruening
    syslog
    Evan Bolyen
    @ebolyen
    Just got q2galaxy running simple commands with the latest master! Unfortunately, there's some warning which get sent to stderr causing the galaxy job to look like it's failed. What's the ideal way to handle that situation?
    Carrie
    @cganote
    @bgruening where is syslog?
    Björn Grüning
    @bgruening
    @cganote /var/log/syslog should be there.
    Evan Bolyen
    @ebolyen
    thanks!
    Carrie
    @cganote
    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
    Björn Grüning
    @bgruening
    OOM killed by?
    Are you running slurm, htcondor or anything fancy like k8s?
    or SGE?
    Carrie
    @cganote
    Just stock docker galaxy. It starts up slurm, right?
    Björn Grüning
    @bgruening
    yes, SLURM by default
    Carrie
    @cganote
    running a STAR job, it's writing arrays to files and dies myseriously
    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
    Björn Grüning
    @bgruening
    @cganote mh, need to look at it and currently only on my mobile
    Tomas
    @TKlingstrom
    I got a vague recolle
    Is it the docker that dies or just the job?
    Evan Bolyen
    @ebolyen
    Is there a way to dynamically serve assets in a Galaxy Visualization tool? We could set up a static service-worker, but that feels like overkill
    Tomas
    @TKlingstrom
    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
    Brad Chapman
    @chapmanb
    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.
    Brad Chapman
    @chapmanb
    Signing off from the day from Boston. There weren't any folks on line for the late check in but would be happy to hear on Gitter what everyone got accomplished for the day. Thanks as always for the hard work and collaboration today.
    Björn Grüning
    @bgruening
    @ebolyen can you explain your idea?
    Evan Bolyen
    @ebolyen
    so I'd like to have a visualization plugin that can load qiime2 visualizations, but it looks like visualization plugins can only host static predetermined assets
    the QIIME 2 visualizations have their own assets but they aren't known ahead of time
    tracking issue: qiime2/q2galaxy#5
    Björn Grüning
    @bgruening
    Mh, I'm the wrong one to ask. @dannon would be better. But this should be possible with the new client work done by Aysam and Dannon.
    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!
    Evan Bolyen
    @ebolyen
    @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
    Björn Grüning
    @bgruening
    I think this should be possible. You can define so called data-providers for every Vis in galaxy. These do usually some conversion for you - you should be able to use them to unpack/mount your datatype with them.
    I will try to get a Vis expert and point him/her in your direction :)
    Evan Bolyen
    @ebolyen
    I thought the data-providers could only do JSON? and thanks so much!
    oh, but it could return the "path", then the problem is just serving that path
    Björn Grüning
    @bgruening
    I think they are more flexible. My understanding is they are used for trackster as well. So indexing datatypes on the fly and so on ...
    Björn Grüning
    @bgruening
    "CLIP-Seq data analysis from pre-processing to motif detection" by Florian Heyl just merged
    galaxy tour is in preparation :)
    Bérénice Batut
    @bebatut
    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.
    Bérénice Batut
    @bebatut
    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