Another recently updated resource for uwsgi is the training slides: https://galaxyproject.github.io/dagobah-training/2018-gccbosc/10-uwsgi/uw... M. On Mon, Jul 9, 2018 at 11:31 AM Peter Briggs <peter.briggs(a)manchester.ac.uk&gt; wrote: > Hello Jochen > > I'm not aware of a tutorial but here are some observations from my (very) > recent experiences upgrading a local paste-based 17.09 instance to a > uwsgi-based 18.05 configuration. It's not comprehensive because the > configuration will depend on decisions you need to make based on your local > setup, but it might be helpful as a starting point. > > Before beginning: > > -- Commit to migrating from galaxy.ini to galaxy.yml (if not done > previously) > > Even though its possible to stick with the old galaxy.ini file, it seems > best to move to the new format - my feeling is, probably the migration will > have to happen at some point anyway, and also the documentation is more > focussed on the newer galaxy.yml version. > > -- Decide on how you're going to handle job submission (essentially, how > you're going to replace the old job handler processes). > > There are a number of possibilities outlined in the documentation here: > > > https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#deploy... > > It seems important to figure this out at the beginning because it impacts > a lot of the configuration specifics that follow. For our setup case "uwsgi > + mules" looked like the most appropriate: > > > https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uwsgi-... > > Then once you're ready to start (nb backing up the database etc before > starting are implicitly assumed!): > > -- Update the Galaxy source code > > The standard recipe for this seems to work okay i.e. > > git fetch origin && git checkout release_18.05 && git pull --ff-only > origin release_18.05 > > (You'll probably also need to run scripts/common_startup.sh to update the > Python packages, and scripts/manage_db.py to update the database schema.) > > -- Create galaxy.yml and configure the "galaxy" section: > > You can make a galaxy.yml from the sample version and go through the > "galaxy" section replicating the settings from galaxy.ini. (The settings in > the "uwsgi" section can wait at this stage.) > Don't forget to move galaxy.ini out of the way once you're done. > > -- Configure the "uwsgi" section of galaxy.yml: > > The options for various scenarios are given in the "Deployment/uwsgi" > section: > > https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uwsgi > > but the required settings seem to be spread out between different sections > so (for me) it felt like it took some piecing together to get it to work > when I first tried this. > > (Also I was thrown a little by the "socket" parameter not having a > placeholder in sample galaxy.yml.) > > The core uwsgi options are here: > > > https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#config... > > then you need to set other options dependent on: > > 1. how job submission is handled (e.g. options for the "uwsgi + mules" > setup in my case) > 2. how you're proxying Galaxy (for Apache or nginx it looks like it's just > setting the uwsgi "socket" option, unless you're serving Galaxy from a URL > prefix in which case there are a few more options needed - these are > covered in the documentation.) > > -- Fix your job_conf.xml file > > If you have an existing job_conf.xml file in your config directory then > you might need to update that too (specifically the "handlers" section) > depending on the job submission handling you've decided to use. > > -- Use supervisor to manage your uwsgi processes > > The docs for this are here: > > > https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#starti... > > Essentially supervisor replaces "run.sh", so this becomes how you start > and stop Galaxy (e.g. "supervisorctl start galaxy:" replaces > "GALAXY_RUN_ALL=1 sh run.sh --daemon".) > > I think this is quite straightforward from the docs but again you need to > tailor it for how you're handling job submission (e.g the "uwsgi + mules" > doesn't need any handlers defining, but it looks like other strategies > needs extra stuff defining here). > > -- Set up the proxying > > Assuming you're proxing via either Apache or nginx (we're using nginx), > these are covered in the relevant sections: > > https://docs.galaxyproject.org/en/release_18.05/admin/apache.html > https://docs.galaxyproject.org/en/release_18.05/admin/nginx.html > > The main difference I noticed for nginx is that you no longer need to use > the "upstream"/"proxy_pass" directives, as nginx can talk directly to uwsgi > using a "uwsgi_pass" directive that connects to the socket defined in the > "uwsgi" section of galaxy.yml previously. > > (There's also a "gotcha" if you're nginx configuration also tries to serve > "static/scripts/packed", which needs to be removed - this is noted in the > "breaking changes" for the 18.05 docs but is easy to miss.) > > Hopefully this is some help. There's lots of documentation, which is a > good thing but which can sometimes make it harder to see where to start. > > Good luck with the update, > > Best wishes > > Peter > > -- > Peter Briggs peter.briggs(a)manchester.ac.uk > Bioinformatics Core Facility University of Manchester > B.1083 Michael Smith Bldg Tel: (0161) 2751482 > > > ________________________________________ > From: galaxy-dev [galaxy-dev-bounces(a)lists.galaxyproject.org] on behalf > of Jochen Bick [jochen.bick(a)usys.ethz.ch] > Sent: Monday, July 09, 2018 12:49 PM > To: galaxy-dev(a)lists.galaxyproject.org > Subject: [galaxy-dev] From Paste to uWSGI > > Hi all, > > we would like to update to 18.05 and thereby also update our Paste Server. > > https://docs.galaxyproject.org/en/latest/admin/scaling.html > > Is there any tutorial on how to update from Paste to uWSGI? > > > Cheers Jochen > > -- > ETH Zurich > *Jochen Bick* > Animal Physiology > Institute of Agricultural Sciences > Postal address: Universitätstrasse 2 > <https://maps.google.com/?q=Universit%C3%A4tstrasse+2&entry=gmail&... > / LFW B 58.1 > 8092 Zurich, Switzerland > Office: Eschikon 27 > 8315 Lindau, Switzerland > > Phone +41 52 354 92 06 <+41%2052%20354%2092%2006> > jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> > www.ap.ethz.ch > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. 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