/netpyne_docker

Export your NetPyNE network model to a Docker container

Primary LanguagePython

Build a Docker container for your NetPyNE model

Use this script to export a NetPyNE model into a Docker container.

Requirements:

  • A netpyne model uploaded to github.
  • a mod folder in the root directory within the github repo (in order to have the mod files already compiled ones you run the container).
  • Docker installed in your personal computer.

Instructions:

create the image:

  • Clone this repo.
  • Launch the Docker app in your machine.
  • Open a terminar and go inside netpyne_docker folder.
  • Type: python netpyne_docker container_tag model_github_repository

NOTES: container_tag is the name you will give to your Docker container. model_github_repository is the github URL where you are sharing your model.

run the container:

  • docker run -it container_tag bash

exit from container:

  • exit

run your python model (when your are inside the container):

  • python init.py

Container packages

  • Linux (Devian)
  • NEURON (7.6.2)
  • Miniconda3 (Python 3.7)
  • NetPyNE (develpment_py3)
  • pyNeuroML

NOTES:

  • Type in a termina source activate snakes to log into the virtual environment that contains NEURON and NetPyNE.
  • The mod files will be already compiled ones you open the container.
  • The building will run in the background, so check the out.log and err.log files.

Docker 101:

  • get docker containers: docker ps
  • delete all images: docker system prune -a (removes absolutely everything)
  • get list of images: docker images -a
  • kill all active containers: docker kill $(docker ps -q)
  • remove all containers: docker rm $(docker ps -a -q)
  • remove all images: docker rmi $(docker images -q)