Name: cycif-benchmarking-docker-ashlar
Owner: sorgerlab
Description: Docker build for benchmarking ASHLAR for AWS Batch
Created: 2018-04-11 17:44:22.0
Updated: 2018-04-12 15:50:28.0
Pushed: 2018-04-17 17:46:47.0
Homepage: null
Size: 4
Language: Python
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This Docker image is designed for use within AWS BATCH.
A YAML file containing the configuration for a job must be provided to the container. Each configuration has the form:
ts:
s3://example/dataset1/raw/cycle1.rcpnl
s3://example/dataset1/raw/cycle2.rcpnl
ut: s3://example/dataset1/ashlar/
ments:
/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.
This image can be used locally as long as appropriate environment variables are set when instantiating the docker container.
ssing the configuration file's location in S3
er run \
AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
AWS_SESSION_TOKEN="${AWS_SESSION_TOKEN}" \
cif-benchmarking-ashlar:latest \
://example/config.yml
ssing the configuration as an environment variable
er run \
AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
AWS_SESSION_TOKEN="${AWS_SESSION_TOKEN}" \
"CONFIG=$(<config.yml)" \
cif-benchmarking-ashlar:latest
It is recommended to use a session token inside the Docker container, which can be generated using the AWS CLI.
sts get-session-token