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Scipion web production setup

Production environment

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 are 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/ 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 are in scipion/etc/service.cfg

—- Movies upload

This feature is currently supported by /services/scipion-mws

In upcoming releases, it may 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

Cloning the production environment

Clone the service an ps-scripts repos (there are snapshots of them [here] vand [here]). First clone the scipion (web) service repository, then inside it, the ps-scripts repository. We recommend 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,


(If needed, use sudo to run the command.)


/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 split 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


/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 are any issues during the installation, you can check the logs at /services/scipion/log

Restart (Bounce)

/services/scipion/etc/service-manager restart

Scipion deployments

For single-user (“private”) use, Scipion can be deployed anywhere; for example, in the user’s home directory. On multi-user machines, the preferred 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 preferred path is /gpfs/fs1/apps/scipion