Edit the bibigrid.properties file provided in the repository and add your ceredentials and path to your SSH key file.
Start bibigrid:
bibigrid.sh -c -o bibigrid.properties
Login to master node (see BiBiGrid output how to set environment variables):
ssh -i ~/.ssh/cmg_ec2euwest.pem ubuntu@ec2-???.???.???.???.eu-west-1.compute.amazonaws.com
Clone the Docker Kraken Pipeline from Github:
git clone https://github.com/asczyrba/docker-kraken.git
Build the Docker image (optional, image is hosted by Docker Hub already):
sudo docker build -t "asczyrba/kraken" .
sudo docker push asczyrba/kraken
Start the pipeline:
Small example (4GB Kraken DB, 10 mio reads in FASTQ file): This qsub command assumes that you have 3 compute nodes with 8 cores each.
/vol/kraken/docker-kraken/scripts/submit_kraken_pipeline.sh 3 8 s3://bibicloud-demo/kraken-db/minikraken_20140330.tar s3://bibicloud-demo/HMP_Stool_Sample/SRS011405_10M.fastq /vol/spool /vol/scratch
Large example (150 GB Kraken DB, 50 mio reads in FASTQ file): This qsub command assumes that you have 10 compute nodes with 32 cores each.
/vol/kraken/docker-kraken/scripts/submit_kraken_pipeline.sh 10 32 s3://bibicloud-demo/kraken-db/kraken_standard.tar s3://bibicloud-demo/HMP_Stool_Sample/SRS011405_50M.fastq /vol/spool /vol/scratch
After logout, terminate the BiBiGrid cluster:
bibigrid.sh -l
bibigrid.sh -t CLUSTERID