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Gustav Ahlberg
@gustavahlberg
Is there anyone here?
bah
galaxybot
@galaxybot
[dave_b] a lot of us run on US time, I won't even be in the lab for another half hour
Björn Grüning
@bgruening
@gustavahlberg hi!
What is ligt?
galaxybot
@galaxybot
[dave_b] my guess would be a finger slipped when typing "lift over"
Nicola Soranzo
@nsoranzo
I think there's now a better tool than lift over, don't remember the name
galaxybot
@galaxybot
[unknown]
Lift-over Convert genome coordinates [Uncategorized]
I’m attempting to use the liftover function on but no matter which file I use, the “To” parameter tells me that there are no options availa…
Björn Grüning
@bgruening
Crossmap
Nicola Soranzo
@nsoranzo
That, thanks! @gustavahlberg see above
Gustav Ahlberg
@gustavahlberg
@nsoranzo @bgruening Thanks
selten
@selten
Today I decided to update to 19.09 and switch to Python 3 (3.7 to be precise), however when I try to access Galaxy I get the following message in the logs: --- no python application found, check your startup logs for errors ---
Nicola Soranzo
@nsoranzo
How do you start Galaxy?
galaxybot
@galaxybot

[unknown]
bowtie2 fatal error message [usegalaxy.org support] error
Good morning,

I am running a ChIP-Seq (pair-end) analysis for the first time and managed to find a good pipeline to follow. The pipeline is…

selten
@selten
./run.sh --daemon
Helena Rasche
@erasche
we've had that,usually an insane pain to debug.
selten
@selten
Are you running py3?
Helena Rasche
@erasche
nope
ours have been from:
  • dependencies missing
  • threading issue with one library
  • something else I've forgotten
but it basically never logged anything, so, good luck.
selten
@selten
I think I found it already 
Traceback (most recent call last):
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 190, in uwsgi_app
    return galaxy.web.framework.webapp.build_native_uwsgi_app(app_factory, "galaxy")
  File "lib/galaxy/web/framework/webapp.py", line 988, in build_native_uwsgi_app
    uwsgi_app = paste_factory({}, load_app_kwds=app_kwds)
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 163, in app_factory
    webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs)
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 1185, in wrap_in_middleware
    from weberror import evalexception
  File "GLXLOC/galaxy/.venv/lib/python3.7/site-packages/weberror/evalexception.py", line 127
    except ValueError, ve:
                     ^
SyntaxError: invalid syntax
Nolan Woods
@innovate-invent
anyone have experience creating collections via the api? galaxyproject/galaxy#8619
Nolan Woods
@innovate-invent
Does all_fasta.loc work with the object store module? or do I have to load everything into a library?
Jennifer Hillman-Jackson
@jennaj
Need more dev eyes on this Q&A please: https://help.galaxyproject.org/t/setting-an-environment-variable-for-python-tools/1486
Brian Myers
@BrianMy06580520_twitter
Hi all, when I recently add a file to my current directory, it is not listed with the ls or ls -a command, and the error message "no such file or directory" is given whenever I try to call the file in terminal. Any suggestions?
Jennifer Hillman-Jackson
@jennaj
@BrianMy06580520_twitter Is this a Galaxy question? (https://galaxyproject.org) If so, could you provide more context?
Right now it just sounds like your file did not end up where you think it went (when using cp, mv, ln -s, etc) or you might not be in the "to" directory but in the "from". Type "cd" to find out where you are.
Sorry, typed too fast. "cd" will move your location back to wherever your home directory is -- type "pwd" instead to find out where your current working directory is
Jennifer Hillman-Jackson
@jennaj
THEN use "cd <path>" to go to where you think the file was supposed to be. You can always scroll back up through your prior commands to double-check where the file was actually placed
Or do a "find" and search for it :)
likku3
@likku3
Hello ,I am trying to setup galaxy on AWS parallel cluster and I am using slurm as my scheduler to spin tools which are dockerized. I have installed slurm-drama and configured in job_config.xml
problem right now is I am unable to run the tools neither I am getting error in logs nor the job is getting submitted.
If some one can share me to how slurm spins docerized tools in nodes will be very helpful to me
galaxybot
@galaxybot
[unknown]
Global Legal Service Solution - Legacore [usegalaxy.org support] admin
We are the next-generation Global Legal Support Services Company, delivering Medico-legal and Secretarial/Administrative services. Our servi…
Jayaram Kancherla
@jkanche
Hello, We developed a galaxy interactive environment for our visualization tool and I was wondering if there is a way to publish this to the galaxy tool shed ? I found documentation for submitting tools to galaxy but if you can point me to the interactive environments that would be great!
galaxybot
@galaxybot

[unknown]
Access Galaxy API behind proxy. [Uncategorized]
Hello,

I have a version of the galaxy behind a proxy(Apache(Basic Auth Authentication)). I want to use the Galaxy API(i.e. http://\[galaxyHo…

Matt Chambers
@chambm
What's the best way to go about creating a link in Galaxy that would use the API to: 1. Import a shared history and make it active; 2. Open the IE launcher page.; alternately if there is a way to just launch a specific IE directly when the user clicks on the link (using a dummy dataset because our IE doesn't need any input datasets), how do we do that?
galaxybot
@galaxybot
[unknown]
Galaxy not deleting [Uncategorized]
Im trying to delete datasets but not working. I logged out, rebooted computer but still nothing… any advice?
Nolan Woods
@innovate-invent
Is there a specific reason user registration is not allowed via the api?
selten
@selten
I register users via the API by making use of BioBlend
I don't know why you think it isn't allowed
Nolan Woods
@innovate-invent
@selten the api returns not implemented https://github.com/galaxyproject/galaxy/blob/9a970d2a6f6277cb4f599c54153c7e0aa38f54bb/lib/galaxy/webapps/galaxy/api/users.py#L199
are you using an admin api key to create the user?
It basically forces me to use the non api interface to register users
which means I need to hack the csrf token
galaxybot
@galaxybot

[unknown]
ATAC-seq with Genrich [Uncategorized]
Hi there,

I’m following the tutorial for ATAC-seq analysis for the platform. They use Genrich for peak calling but it doesn’t show up when …

selten
@selten
Ah yes @innovate-invent I create it as an admin
I forgot about that part of it
galaxybot
@galaxybot

[unknown]
FreeBayes: installing onto local instance of Galaxy [usegalaxy.org support] freebayes, galaxy-local
I have a local instance of Galaxy 19.01.

From the ToolShed, I installed freebayes 1.1.0.46 (156b60c1530f). When I ran it, the following err…