[galaxy-dev] GalaxyAdmins Meetup This Thursday

Hello all, The June online meetup of GalaxyAdmins will be this Thursday . This month features two talks: *1. Galaxy in Production at the University of Minnesota* [image: Minnesota Supercomputing Institute]

[galaxy-dev] Infinite recursion on conda dependency manager

Hi there I've got a package in our lab conda channel (its still in testing phase) called goget. This is specified as a requirement for the build_ctb_gene tool like this: goget When the tool runs, I see infinite recursion on the conda side: https://gist.github.com/pvanheus/c16a0

Re: [galaxy-dev] History is not up-to-date

Hi, Phillip Quick questions: - is the time properly set on the computer where you've got Galaxy running in the browser? - is the time in the docker container also correct? >From you terminal output it looks like the update time might be the issue and we can then take it from there. Thanks On Tu

Re: [galaxy-dev] how to get raw input from GUI

A general note, besides which sounds like a fine choice, a technique I've used where the form's input might have some wonky characters in it, including carriage returns, but these need to be received and processed via a command line, is to use encode(): $rules.encode('base64').replace('\n','') T

[galaxy-dev] History is not up-to-date

Dear All, I have a problem with my histories.  We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all. however, something is running in the back 129.69.102.30 -

Re: [galaxy-dev] tabular file displayed without tabs

Ok, so it's definitely the column limit that's causing the unexpected style-less display. This currently isn't configurable per-galaxy (the plan was to add more appropriate displays for many-columned files), but here's a quick gist to show you how you might tweak this locally: https://gist.github

Re: [galaxy-dev] tabular file displayed without tabs

No, it happens to all output from this particular tool. I do see a javascript warning in the console, 'The character encoding of a framed document was not declared. The document may appear different if view without the document framing it.' The file does have 64 columns in it. Is there a way to

Re: [galaxy-dev] cleanup datasets error

Wuhu! On 14.06.2016 11:25, Philipp Rathert wrote: RE: [galaxy-dev] cleanup datasets error Hi Bjoern, Works now. Thank you very much, Philipp *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:* Tuesday, June 14, 2016 11:07 AM *To:* Rathert, Philipp, Dr. *Cc:* galaxy-dev *Subj

Re: [galaxy-dev] cleanup datasets error

Hi Bjoern, Works now. Thank you very much, Philipp From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: Tuesday, June 14, 2016 11:07 AM To: Rathert, Philipp, Dr. Cc: galaxy-dev Subject: Re: [galaxy-dev] cleanup datasets error Hi, can you please do this before executi

Re: [galaxy-dev] cleanup datasets error

Hi, can you please do this before executing the script. This will source your Galaxy virtual-env. """ source $GALAXY_VIRTUAL_ENV/bin/activate """ Ciao, Bjoern On 14.06.2016 11:01, Rathert, Philipp, Dr. wrote: RE: [galaxy-dev] cleanup datasets error Hi Bjoern, I edited the galaxy.ini d

Re: [galaxy-dev] cleanup datasets error

Hi Bjoern, I edited the galaxy.ini directly and started the script. Unfortunately I get a different error: Traceback (most recent call last):   File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in     main()   File "scripts/cleanup_datasets/cleanup_datasets.py", line 104,

Re: [galaxy-dev] cleanup datasets error

Hi Bjoern, This is wired. It worked before... I will add this to the galaxy.ini in the config folder and try again. Cheers, Philipp ---Philipp on the road--- Am 14.06.2016 um 09:50 schrieb Bjoern Gruening mailto:bjoern.gruen...@gmail.com> >: Hi, I don't think this will work with the script

Re: [galaxy-dev] cleanup datasets error

Hi, I don't think this will work with the script. This script reads the config file you specify config/galaxy.ini. And hence it needs to be added in this file, not via -e variables. This is probably something we should improve. Ciao, Bjoern cleanup datasets error > > HI Björn, > > > > I h

Re: [galaxy-dev] cleanup datasets error

HI Björn, I have added these to the galaxy.ini via the docker specific e- variables during startup of the container. How can I check if they are broken? Cheers, Philipp From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] Sent: Tuesday, June 14, 2016 9:30 AM To: Rathert, P

Re: [galaxy-dev] cleanup datasets error

Hi Philipp, have you followed this from the readme? Note that if you would like to run any of thecleanup scripts , you will need to add the following to|/export/galaxy-central/config/galaxy.ini|: |da

[galaxy-dev] cleanup datasets error

Dear all, when I want to start the cleanup datasets script I get the following error. (.venv)root@galaxy:/galaxy-central# python /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d -10 -1 Traceback (most recent call last):   File "/galaxy-central/scripts/cl