Is there a Quickstart guide for OpenBIS?

Installation & maintenance
1

I am looking setup OpenBIS as a trial ELN / LIMS system.
I want to try the various user interfaces, and managing data via dropbox and using jupyterhub.

I have been able to run the debian docker container, but can only access the core UI via localhost.
I don’t see documentation regarding default ports/hostnames/paths.

Are there existing quickstart/setup guides that I can follow along?

2

I am working on openBIS demo for openBIS ELN-LIMS Virtual Machine
https://unlimited.ethz.ch/display/openbis/openBIS+ELN-LIMS+Virtual+Machine

This is fully working openBIS setup on VirtualBox.
This for Demo on user’s desktops using GUI but if you know Ubuntu Linux you could use it as reference instance.

Download this Vagrantfile

And you have the VirtualBox instance running. If you know Ubuntu Linux then read the Vagrantfile, I commented it hot to make openBIS running on Ubuntu Linux.

3

Thankyou for your reply.
I originally tried using the VM’s, but I was not clear how to go further regarding setting up juyterhub and configuring dropboxes.
This is why I pivoted to using the docker images - Docker

I am able to run both containers and they appear healthy, but I am having some configuration issues regarding the interaction between openbis and jupyterhub. - I can see the plugin in openbis eln/lims ui is available, but I cannot create new workspace or notebooks.

Regarding the dropboxes, the issue is I am not clear what configuration changes/folders structure needs to be setup to link the data to an experiment.

Is there any documentation / guides that can help me with either issue?

For Jupyterhub, the guide seems outdated/incomplete - JupyterHub for openBIS - openBIS Documentation Rel. 20.10 - Confluence
The image name does not match the repository.

4

Dear @sgallagher,
we have completed documentation for openBIS as a docker container.
https://openbis.readthedocs.io/en/latest/system-documentation/docker/index.html

I have included the Quickstart too for users already familiar with Docker.
https://openbis.readthedocs.io/en/latest/system-documentation/docker/quickstart.html

I see the quickstart minimal enough and working on most environments I have conducted verification on. The only issue I have found so far at some docker environments is connectivity between containers.

It leads to following type of error:

$ docker logs openbis-ingress
Configuration file is valid
[WARNING]  (681) : Server openbis_as/as is DOWN, reason: Layer4 timeout, check duration: 2002ms. 0 active and 0 backup servers left. 0 sessions active, 0 requeued, 0 remaining in queue.
[ALERT]    (681) : backend 'openbis_as' has no server available!
[WARNING]  (681) : Server openbis_dss/dss is DOWN, reason: Layer4 timeout, check duration: 2002ms. 0 active and 0 backup servers left. 0 sessions active, 0 requeued, 0 remaining in queue.
[ALERT]    (681) : backend 'openbis_dss' has no server available!

I will possibly add a “Troubleshooting” section in near future to help us to debug that connectivity issues and any others. Generally the “Verification” described here
https://openbis.readthedocs.io/en/latest/system-documentation/docker/verification.html
is minimal enough to confirm if the environment is set correctly.

In near future I will be working to upgrade our container with JupyterHub preconfigured to easy integrate with openBIS and I will work to update that outdated documentation.

Thank you for your feedback. Sooner or later we will challenge or reported issues.

Regards,
Artur

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