Re: [galaxy-dev] showing progress on running tasks

Hi Ryan, On Sat, Jul 9, 2016 at 12:40 AM, Ryan G wrote: > Hi Martin - I was actually thinking to let the tool itself tell Galaxy about > the progress instead of Galaxy estimating that. > > If instance, if the tool know it has 5 stages, it can report back to Galaxy >

[galaxy-dev] Can't stop uwsgi processes with supervisod

Dear experts, I've a strange behaviour with uWSGI and supervisor. This is my settings in galaxy.ini file: [uwsgi] processes = 3 socket = 127.0.0.1:4001 stats = 127.0.0.1:9191 #socket = /var/log/galaxy/uwgi.sock pythonpath = /home/galaxy/galaxy/lib pythonhome = /home/galaxy/galaxy/.venv threads =

Re: [galaxy-dev] showing progress on running tasks

Hi Ryan, multiple tool stages do not necessarily equally split runtime so you wouldn't have 'time progress bar' but 'unscaled progress bar'. The usefulness of such I would put somewhere in between a loading animation and stats estimate. This would also require every tool to be enhanced as well as

Re: [galaxy-dev] showing progress on running tasks

Hi Ryan, This is a fairly complex problem because the length of the run depends most often on input size, job algorithms, and computational capacity all of which are quite difficult to estimate. We have discussed it before and one of the ways to approach this is to gather statistics from as many

Re: [galaxy-dev] Metadata access using tool config

Hi Katherine, Probably about the only way to get the job start time is job.create_time (a close estimate to the actual start time) and the end time is job.update_time (again, a close estimate), so you can calculate the job’s estimated execution time using something like this: import datetime

Re: [galaxy-dev] Metadata access using tool config

Actually just figured out the history content api id, just needing the extra stuff about the job like runtime and start and end times. On Fri, Jul 8, 2016 at 8:55 AM, Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > Hi Greg, > Thanks for the link to your github repo, some of the

Re: [galaxy-dev] Metadata access using tool config

Hi Greg, Thanks for the link to your github repo, some of the information there was very useful. Do you have any idea on how to access some of the stuff you don't yourself pass to your python script such as the history content api id, or the job runtime? For example for the job runtime I feel like

Re: [galaxy-dev] Python tool wrapper with multiple input and output files

Hi Marco, The tag has been deprecated, what you should use is just Note the $*tool_directory*, this is required for finding the path to the script. (And that has been “magically” done for you by the tag). Hope that works for you, Marius On 8 July 2016 at 11:43, Marco Tangaro

Re: [galaxy-dev] Python tool wrapper with multiple input and output files

Dear Marius and all, thanks a lot for your answer, it is indeed very interesting. I'm following this one https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml to create an output list, starting from an input list. The command section of my