Running locally¶

The Reservoir Genome Browser can be run locally to view files on your computer without uploading to the hosted instance at resgen.io.

Usage requires a license. If you already have a resgen subscription, you can get a license from resgen.io.

If you don't have a license, you are entitled to run locally and host directories with a maximum of 10 datasets.

Starting locally¶

Starting locally will start resgen as a server on your local computer. You can access the UI at http://localhost:1807 (The port can be changed using the --port flag in the commands below)

resgen manage start ~/my-directory

If you are on an M* Mac you'll need to add --platform=linux/arm64/v8 for the right Docker image to be used.

resgen manage start ~/my-directory --platform=linux/arm64/v8

Create local user¶

Even when running locally you need to set up a user:

resgen manage create-user ~/my-directory

Synchronize datasets¶

Resgen maintains its own database of datasets, you'll need to synchronize manually when anything is added to the directory outside of resgen.

resgen manage sync-datasets ~/my-directory

Getting logs¶

If an error occurs, you can get the latest logs:

resgen manage logs ~/my-directory [nginx,uwsgi,celery]

The last parameter specifies the service to get logs for. In the majority of cases this will be uwsgi.

Advanced functionality¶

Creating a superuser¶

A superuser can use the admin interface to modify users, projects and datasets.

resgen manage create-superuser ~/my-directory

Starting with a non-standard image¶

One may wish to start resgen with an older image:

resgen manage start --image <image_name> ~/my-directory

Viewing a dataset¶

Use the resgen manage view command to view local datasets.

Displaying a sequence logo¶

The following command will generate a sequence logo plot from the 4th (1-based) column in the given csv file.

resgen manage view simulated_sars2_spike_15.csv \
  -t colnum:4 \
  -tt sequence-logo \
  -tp top

The extra options are:

-t - Add a tag to the created dataset saying to use column number 4. It's also possible to use -t colname:blah to tell it to use the column name blah
-tt - The track type to use (sequence-logo)
-tp - Position this track up top. As opposed to on the left or right