What is this

batch-titration is a container allows for one or more fcs files to be automatically processed (using AWS Batch or other runners). It consists of an R package, some scripts, and a Dockerfile. It produces an html document.

This software was presented in our TiterCheck poster at CYTO2018 https://figshare.com/articles/Method_for_Monitoring_Status_of_Antibody-Fluorochrome_Conjugates_For_Accurate_Enumeration_of_Extracellular_Vesicles/6719837

How to dockerize batch-titration

devtools::build()

This will produce a .tar.gz in the directory above the package directory

cd ..
ln -s batch_titration/Dockerfile .
aws ecr get-login --no-include-email --region us-east-1
# run that
docker build -t cytovas-batch-titration .
docker tag cytovas-batch-titration:latest 205853417430.dkr.ecr.us-east-1.amazonaws.com/cytovas-batch-titration:latest
docker push 205853417430.dkr.ecr.us-east-1.amazonaws.com/cytovas-batch-titration:latest

As an aside, to clean up docker

docker ps -aq -f status=exited
docker ps -aq --no-trunc | xargs docker rm
docker images -q --filter dangling=true | xargs docker rmi

To test locally and override snakemake

docker run -it --entrypoint "/bin/bash" -e AWS_ACCESS_KEY_ID="your access key" -e AWS_SECRET_ACCESS_KEY="your secret" -e CONFIG_KEY="40cfa138-b869-4a16-a854-e50636a5e43e.yaml" cytovas-batch-titration

To run from Amazon ECR

aws ecr get-login --no-include-email --region us-east-1

(run this login command)

To add local mounts to docker ()

docker run -it -v /projects:/projects 205853417430.dkr.ecr.us-east-1.amazonaws.com/cytovas-batch-titration /usr/local/lib/R/bin/R 

You can then

library("batchTitration")

To queue a AWS batch job. The CONFIG_KEY refers to a config file in the titration config bucket.

aws batch submit-job --job-name example --job-queue fcs-batch-queue  --job-definition batch_titration_or_check --container-overrides '{"environment":[{"name":"CONFIG_KEY","value":"40cfa138-b869-4a16-a854-e50636a5e43e.yaml"}]}'

List the jobs:

aws batch list-jobs --job-queue arn:aws:batch:us-east-1:205853417430:job-queue/fcs-batch-queue

To monitor a job

aws batch describe-jobs --jobs 7bcd65c8-a74d-4c26-a1aa-a5bb716b4963