Scipion web production setup
This setup uses tools that are production-ready and support the requirements of a web service in the Internet (which are quite different from a small local service for testing)
All the service needs is self-contained in the service directory. For simplicity, this directory is called "scipion", so the typical path to the service would be /services/scipion
While everything is nicely organized, you can find the mandatory
introductory documentation in the scipion/README.md file
The current frontend is an apache server, and the current application
server is Gunicorn. You can manage (start, restart…) both services
with the scipion/scripts/apache-service and
scipion/etc/scipion-manager scripts.
The service as a whole is managed with scipion/etc/service-manager. It
is the perfect starting point to learn the latest state of things
regarding configuration and how everything works (what it is needed and
when)
All the relevant configuration is in scipion/etc. For example, apache
configuration, backup configuration, roles, permissions…
One key setting is which scipion software installation to use. Set it in
the ${scipion} variable (in scipion.env, through the $PW_HOME
variable).
Other more general service settings live in scipion/etc/service.cfg
---- Movies upload
This feature is currently supported by /services/scipion-mws
Maybe in next releases it will be integrated into scipion service.
Again, all config is in scipion-mws/etc, and you can dive into the
details from scipion-mws/etc/service-manager
Clone the service an ps-scripts repos (there are snapshots of them
here and
here). First clone the
scipion (web) service repository, then inside it, the ps-scripts
repository. We recomend to use /services as base directory, hence after
the 2 clones, you should find /services/scipion/scripts,
/services/scipion/scripts/etc, …
Edit etc/service.cfg and update the service and service_root
parameters.
Run the service-create script using its absolute path, and follow its
instructions. For example,
/services/scipion/service-create
(If needed, use sudo to run the command.)
Run
/services/scipion/scripts/config/apache2/mkhttpd_conf > /services/scipion/etc/apache/httpd.conf
/services/scipion/scripts/config/apache2/mkservice_conf > /services/scipion/etc/apache/service.conf
and check service.conf to ensure all paths are correct.
Currently, scipion-specific config is splitted across 3 different places:
-
etc/scipion-config/*.conf: global configuration (in theory) -
usr/scipion/config/*.conf: global configuration (of the scipion instance in use) -
data/scipionweb/.config/scipion: configuration of each of the web tools.
Check/edit all these scipion config files above.
Regarding the projects data, you need to clone the directories
data/scipionweb/ScipionUserData/(movies,myfirstmap,myresmap)
For the tests data, you need to run (as scipionweb user):
/services/scipion/usr/scipion/scipion testdata --download riboMovies
Run
/services/scipion/etc/service-manager start
This script will check if all the software dependencies for the services are installed (and install the missing ones)
If there is any issue during the installation, you can check the logs at
/services/scipion/log
Scipion deployments
For single-user ("private") use, Scipion can be deployed anywhere, for example in the user’s home directory. In multi-user machines, the prefered location is /usr/local/scipion. In cluster environments, Scipion should be installed in the shared filesystem, so all nodes have access to it. In crunchy, for example, the prefered path is /gpfs/fs1/apps/scipion
— Main.JesusCuenca - 2013-07-31