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Nicola Soranzo
@nsoranzo
@hepcat72 https://docs.galaxyproject.org/en/master/admin/jobs.html
galaxybot
@galaxybot
[mrscribe] Title: Galaxy Job Configuration Galaxy Project documentation (at docs.galaxyproject.org)
Robert Leach
@hepcat72
Thanks @nsoranzo !
Nate Coraor
@natefoo
if there's no entry for the tool then it's probably using a default, although if you have dynamic destinations defined then it could be set in one of those rules
Steven Weaver
@stevenweaver
Hey guys, just wanted to say that I’m impressed by the .travis.yml build script for tools-iuc and extensive galaxyproject documentation. :+1:
Peter Cock
@peterjc
Anyone here using Kraken and/or Kaiju? I've started work on defining Galaxy datatypes for their databases - see galaxyproject/galaxy#5704 - feedback welcome. Thanks!
galaxybot
@galaxybot
[mrscribe] Title: Define kaiju_db and kraken_db as compound datatypes [WIP] by peterjc · Pull Request #5704 · galaxyproject/galaxy · GitHub (at github.com)
Robert Leach
@hepcat72
So I believe I have made the necessary addition to job_conf.xml. Lance is the one who always restarts galaxy. I've done it on my own instance on my machine, but I don't know what the risks are of me doing it on our production server. Is there anything special someone could do other than running run.sh - like are there special options or something someone might always do? Do I need to be concerned about what user is running run.sh?
Nate Coraor
@natefoo
it's probably not using run.sh
Robert Leach
@hepcat72
Ah
OK
Nate Coraor
@natefoo
try using pstree to see what's running galaxy.
Robert Leach
@hepcat72
What am I looking for in the output? Thanks for the hand-holding, BTW ;)
python?
Nate Coraor
@natefoo
yeah it'll probably be python, or uwsgi. the -a option to pstree is useful
Robert Leach
@hepcat72
Wait, Lance just logged into Slack. I think I'll have it from here
Nicola Soranzo
@nsoranzo
You can also look for galaxy.ini probably
Nate Coraor
@natefoo
is there a reason single-line tabular data is not considered tabular? https://github.com/galaxyproject/galaxy/blob/8366d2b5fa32c5697306139426d85df86dac0782/lib/galaxy/datatypes/sniff.py#L272
galaxybot
@galaxybot
[mrscribe] Title: galaxy/sniff.py at 8366d2b5fa32c5697306139426d85df86dac0782 · galaxyproject/galaxy · GitHub (at github.com)
Micropathology
@Micropathology
@mvdbeek I have updated galaxy and conda, now I still get issue Fatal error: Exit code 1 ()
Error: Unspecified error with Unicycler dependencies
Micropathology
@Micropathology
I have run some of the other other newly installed tools such a prokka and now i get
atal error: Exit code 2 ()
Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /mnt/galaxy/tool_dependencies/_conda/envs/__prokka@1.12/lib/site_perl/5.26.0/x86_64-linux-thread-multi /mnt/galaxy/tool_dependencies/_conda/envs/__prokka@1.12/lib/site_perl/5.26.0 /mnt/galaxy/tool_dependencies/_conda/envs/__prokka@1.12/lib/5.26.0/x86_64-linux-thread-multi /mnt/galaxy/tool_dependencies/_conda/envs/__prokka@1.12/lib/5.26.0 .) at /mnt/galaxy/tool_dependencies/_conda/envs/__prokka@1.12/bin/prokka line 25.
BEGIN failed--compilation aborted at /mnt/galaxy/tool_dependencies/_conda/envs/__prokka@1.12/bin/prokka line 25.
so there are some changes but still problems
John Chilton
@jmchilton
Jenkins is testing a bunch of random old already merged PRs today - for apparent reason :(
Dannon
@dannon
I thought I configured cancel-on-merge for at least some stuff a while bacfk
Or maybe it was just cancel on branch push, to interrupt and restart? I dunno.
John Chilton
@jmchilton
Its not for PRs merged today - they were merged a while ago I think. I'll see if I can find a pattern - probably just a bug in Jenkins
Dannon
@dannon
Oh weird.
Nicola Soranzo
@nsoranzo
@jmchilton galaxyproject/galaxy#5701 seems to properly save the available artifacts, correct?
John Chilton
@jmchilton
@nsoranzo Yeah - looks good to me https://jenkins.galaxyproject.org/job/docker-selenium/1695/artifact/1695-test-errors/
galaxybot
@galaxybot
[mrscribe] Title: Artifacts of docker-selenium #1695 : /1695-test-errors [Jenkins] (at jenkins.galaxyproject.org)
Nicola Soranzo
@nsoranzo
Just wanted to double check with you, merging now.
John Chilton
@jmchilton
Thanks for the help with that by the way
Nicola Soranzo
@nsoranzo
Sure thing
Ghost
@ghost~5772e7e2c2f0db084a206e1b
@Micropathology what command did you use to install unicycler ?
Can you look at the installation log for prokka ?
Nate Coraor
@natefoo
is static/style/blue/base.css supposed to exist in dev?
Dannon
@dannon
Yes.
Only static/scripts were dropped. We left style since it changes so much less often.
(and is much more of a pain to add style and the various artifacts back in release branches)
Nate Coraor
@natefoo
ah
it changes all the time when developing which is a little annoying
Dannon
@dannon
Ideally we drop that, along with even more stuff, down the road though as the auto-building/etc gets a real test and seems to be robust enough.
It should only change if someone in a commit before you forgot to add it, or if you're changing styles?
Nate Coraor
@natefoo
i'm not sure why it differs since i'm not changing ... yeah.
could be due to different versions of the build tools
Dannon
@dannon
Possible. I'm overhauling that a lot right now in my bs4 branch, hopefully a few more steps towards it being robust enough to drop.
Nate Coraor
@natefoo
cool
Dannon
@dannon
(it almost looks like Galaxy again!)
Nate Coraor
@natefoo
haha