CycIF Benchmarking - ASHLAR

This Docker image is designed for use within AWS BATCH.

Job configuration YAML

A YAML file containing the configuration for a job must be provided to the container. Each configuration has the form:

inputs:
  - s3://example/dataset1/raw/cycle1.rcpnl
  - s3://example/dataset1/raw/cycle2.rcpnl
output: s3://example/dataset1/ashlar/
arguments:
  - /mnt/input/*.rcpnl

All inputs are copied into the /mnt/input directory in the Docker container. If an input is suffixed with a / it is recursively copied to /mnt/input so that the relative directory structure is maintained.

arguments is passed directly to ashlar so a series of options can be specified as a list. No default is provided to ashlar for the required filepaths positional argument so this must be specified.

This configuration file's location in S3 is passed to the docker container as the only argument or can alternatively be passed as a string in the environment variable CONFIG.

Local usage

This image can be used locally as long as appropriate environment variables are set when instantiating the docker container.

# Passing the configuration file's location in S3
docker run \
  -e AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
  -e AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
  -e AWS_SESSION_TOKEN="${AWS_SESSION_TOKEN}" \
  cycif-benchmarking-ashlar:latest \
  s3://example/config.yml

# Passing the configuration as an environment variable
docker run \
  -e AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
  -e AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
  -e AWS_SESSION_TOKEN="${AWS_SESSION_TOKEN}" \
  -e "CONFIG=$(<config.yml)" \
  cycif-benchmarking-ashlar:latest

It is recommended to use a session token inside the Docker container, which can be generated using the AWS CLI.

aws sts get-session-token