Skip to content

Latest commit

 

History

History
168 lines (110 loc) · 4.88 KB

GVL4.1_to_uswgi.md

File metadata and controls

168 lines (110 loc) · 4.88 KB
Raw

Upgrade GVL 4.1 to use uswgi instead of paster.

This lays out how to get the Galaxy server in GVL 4.1 running using the new uwsgi webserver instead of the old paster one. It will also install and configure supervisor to control galaxy start/stops.

  • It will by default change the way galaxy works. We will set up a galaxy webserver and two galaxy headless handler services using the galaxymain script that comes with Galaxy.

  • It will require some changes to the job_conf.xml file to include these new handlers.

NOTES:

  • This will make the galaxy server non-repsonsive to commands from Cloudman. i.e. You won't be able to restart it from cloudman any longer.. A fix for this will require some changes to cloudman to make it use supervisor..

Installations

We need to install a few things before we can begin... Namely uwsgi, its python libraries and supervisor.

sudo apt install uwsgi uwsgi-plugin-python supervisor

Then we need to install the uwsgi decorators to the galaxy python virtualenv..

sudo -Hu galaxy /mnt/galaxy/galaxy-app/.venv/bin/pip install uwsgidecorators

Configure uwsgi

galaxy.ini

Add the following to /mnt/galaxy/galaxy-app/config/galaxy.ini. Put it above the [server:main] section.

[uwsgi]
processes = 2
threads = 2
socket = 127.0.0.1:4001     # uwsgi protocol for nginx
pythonpath = lib
master = True
logto = /mnt/galaxy/galaxy-app/uwsgi.log
logfile-chmod = 644

Also, make sure that there is a line in galaxy.ini that tells Galaxy about the location of the job_conf.xml file:

job_config_file = /mnt/galaxy/galaxy-app/config/job_conf.xml

Configure job handlers

job_conf.xml

Edit the /mnt/galaxy/galaxy-app/config/job_conf.xml file and change the entire

<handlers ...>
  ...
</handlers>

section to:

<handlers default="handlers">
    <handler id="handler0" tags="handlers"/>
    <handler id="handler1" tags="handlers"/>
</handlers>

Configure nginx

Configure the nginx configuration for galaxy so it uses uwsgi socket bindings instead of paster.

Edit the galaxy.locations file:

sudo vim /etc/nginx/sites-enabled/galaxy.locations

Change the location /galaxy { section so it looks like:

        location /galaxy {
            #proxy_pass  http://galaxy_app;
            #proxy_set_header   X-Forwarded-Host $host;
            #proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
            uwsgi_pass           127.0.0.1:4001;
            include              uwsgi_params;
        }

Unfortunately, Cloudman will overwrite these changes so chmod -w this file with to prevent it.

Then restart nginx with sudo service nginx restart

Stop old Galaxy

Now you need to stop Galaxy (if you haven't already)...

from the /mnt/galaxy/galaxy-app directory:

sudo -Hu galaxy ./run.sh --log-file=main.log --pid-file=main.pid --stop-daemon

Setup supervisorctl

Now configure supervisor so that it can start/stop the Galaxy web front end and the two job handlers (headless Galaxys)..

Check to see if supervisor is running:

sudo supervisorctl status

If its running it will return it's status..

Now we need to configure a galaxy supervisor control file..

Create/edit the following file:

sudo vim /etc/supervisor/conf.d/galaxy.conf

add the following:

[program:galaxy]
command         = uwsgi --plugin python --virtualenv /mnt/galaxy/galaxy-app/.venv --ini-paste /mnt/galaxy/galaxy-app/config/galaxy.ini
directory       = /mnt/galaxy/galaxy-app
autostart       = true
autorestart     = true
startsecs       = 10
user            = galaxy
stopsignal      = INT

[program:handler]
command         = /mnt/galaxy/galaxy-app/.venv/python /mnt/galaxy/galaxy-app/scripts/galaxy-main -c /mnt/galaxy/galaxy-app/config/galaxy.ini --server-name=handler%(process_num)s --log-file /mnt/galaxy/galaxy-app/handler%(process_num)s.log
directory       = /mnt/galaxy/galaxy-app
process_name    = handler%(process_num)s
numprocs        = 2
umask           = 022
autostart       = true
autorestart     = true
startsecs       = 10
user            = galaxy
environment     = VIRTUAL_ENV="/mnt/galaxy/galaxy-app/.venv",PATH="/mnt/galaxy/galaxy-app/.venv/bin:%(ENV_PATH)s"

[group:gx]
programs = galaxy,handler

Now just update supervisor to get it all running..

sudo supervisorctl update

Controlling Galaxy

Start

sudo supervisorctl start gx:*

Stop

sudo supervisorctl stop gx:*

Restart

sudo supervisorctl restart gx:*

It can be a bit more nuanced than that.. For example to just restart Galaxy's webapp: sudo supervisroctl restart gx:galaxy and to just restart one of the job handlers (say handler0): sudo supervisorctl restart gx:handler0

Log files

Galaxy's log files are now threefold. One for the webserver app and one each for the two headless job handlers.. They are now located as follows:

/mnt/galaxy/galaxy-app/uwsgi.log
/mnt/galaxy/galaxy-app/handler0.log
/mnt/galaxy/galaxy-app/handler1.log