registry: List of Docker containers for LSP pipelines

Full list on Dockerhub: https://hub.docker.com/u/datarail/

Current containers:

• concat - "Hello World" example demonstrating the usage of Docker and docker-compose. [GitHub]
• pamsig - Clusters segmented CyCIF data using Partitioning Around Medoids (PAM) and produces signatures that define each cluster. [GitHub][Example data]

Instructions for Developers

Prepare

1. Set up your code to be executable from command line.
2. Modify your code to read all input from /input/ and write all output to /output/
3. Have your code read method-specific parameter settings from /config/<container name>.yml

Package

1. Put together a Dockerfile that installs and configures all the necessary dependencies for containerizing your code. See examples for Python and R.
2. cd into the directory containing the Dockerfile.
3. Build your container by running docker build -t datarail/<container name> .
4. Verify locally that your container runs as expected by executing docker run -v <path to config>:/config -v <path to data>:/input -v <path to results>:/output datarail/<container name> or by using a docker-compose file (see concat for an example).

Deploy

1. Upload your code to a GitHub repository. Include an example config file, example docker-compose.yml (preferably making use of the example data) as well as a README that describes the expected arguments and/or environment variables.
2. Create a DockerHub account. Contact Jeremy, Douglas or Artem to be added to the datarail group.
3. Configure a DockerHub repository for the Docker image to automatically build the master branch and tags of the GitHub repository on commit (https://docs.docker.com/docker-hub/builds/).
4. Send an e-mail to @ArtemSokolov with a one-paragraph description of your method and a link to your GitHub repo.

Exemplify

It is strongly recommended to create an exemplar dataset to be used with your container. Currently, LSP hosts exemplar data for Datarail pipelines in AWS S3 buckets. To upload your data, post in the @aws Slack channel requesting to be added to our AWS organization. After getting access, upload your data to datarail-example-data/<container name>/. Please provide instructions in the application README on how to download the examplar data in preparation for using the exemplar docker-compose file.