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danielm710 edited this page Mar 11, 2021 · 7 revisions

Unable to start Docker

If you are unable to use Docker and Docker-Compose due to Permission issue, adding yourself under docker group in the system may solve the issue.

Follow the instruction below:

  1. Check docker group exists in your system
cat /etc/group | grep docker

If the command above returns docker​ , proceed to Step 2. If the command above returns nothing, you will need to create a group called docker in your system.

sudo groupadd docker
  1. Add a user (yourself) to the docker group
sudo usermod -aG docker YOUR_USER_NAME

For example, if your user name is Foo, the command would be

sudo usermod -aG docker Foo

You can find your user name with the command, whoami.

  1. Log out and re-log back in to apply the group setting.
  2. Run docker run hello-world to test it's working.

Installation Error

At the end of the installation, if you see a message like below,

Creating axiome3-gui_backend_1          ... error
Creating axiome3-gui_rabbit_1  ... 
Creating axiome3-gui_extension_worker_1 ... 
Creating axiome3-gui_pipeline_worker_1  ... 

Creating axiome3-gui_rabbit_1           ... done
Creating axiome3-gui_extension_worker_1 ... done
Creating axiome3-gui_pipeline_worker_1  ... done

ERROR: for backend  Cannot create container for service backend: failed to mkdir /var/lib/docker/volumes/axiome3-gui_pipeline_volume/_data/.git/branches: mkdir /var/lib/docker/volumes/axiome3-gui_pipeline_volume/_data/.git/branches: file exists
ERROR: Encountered errors while bringing up the project.

Restarting AXIOME3 should often solve the issue. docker-compose -f docker-compose_production.yml up -d.

Docker on Windows/Mac out of resource

Docker on MacOS has default resource limit (CPUs and RAM) which is not enough to run Denoise and Analysis modules in AXIOME3. You need at least 16GB (and much more depending on your dataset size) and more CPUs if you want to parallelize your workflow. You may change this in Docker Desktop under Settings (gear icon in the top right side of the window) -> Resources -> Advanced

Queuing system stops working

Sometimes, AXIOME3's queuing system stops working for no obvious reasons... In this case you would have to restart AXIOME3.

You may run the following commands in order to restart AXIOME3,

1. docker-compose -f docker-compose_production.yml down (this command shuts down the app)
2. docker volume prune (this command removes any attached volumes)
3. docker-compose -f docker-compose_production.yml up -d (this starts the app again)

Maximum possible number of colours to render in the Extension module

Currently, maximum 12 groups can be visualized with different colours in the Extension module.

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