docker-kraken-gcb

Start BiBiGrid Cluster

First, we need to start a bibigrid cluster in the cloud. If you have not done this already, edit the properties file downloaded from the gcb-tutorial repository and add your credentials and path to your SSH key file.

Start bibigrid:

bibigrid -u $USER -c -o bibigrid.properties

Login to master node (see BiBiGrid output how to set environment variables):

ssh -i ~/.ssh/SSH_CREDENTIALS.pem ssh -i id_rsa ubuntu@$BIBIGRID_MASTER

Download Github repository

Now your are logged on to the master node of your cloud-based SGE cluster! We will clone the docker-kraken-gcb github repository to the master node and continue working on the master node.

Clone the Docker Kraken Pipeline from Github:

cd /vol/spool
git clone https://github.com/bibiserv/docker-kraken-gcb.git
cd docker-kraken-gcb

Set environment variables

The command line calls on this page assume that you have several environment variables set for your cloud environment. This makes it easier to copy & paste the commands:

export NUM_NODES=4
export NUM_CORES=4
export HOST_SPOOLDIR=/vol/spool
export HOST_SCRATCHDIR=/vol/scratch
export DOCKER_USERNAME=<DOCKERHUB ACCOUNT NAME>

Kraken Docker Image

The Dockerfile includes all information about the Docker image. Place scripts you want to have accessible in the image into the container_scripts directory. These scripts will be called to donwload the database to the hosts and run the analyses.

Login to DockerHub

We need to pull the updated image to each of the hosts before we can start the analysis scripts. Before pushing to the DockerHub, you need to login:

docker login -u $DOCKER_USERNAME

Building and Pushing the Docker Image

Now every time you made a changes to the container scripts, you need to push the image to DockerHub:

docker build -t "$DOCKER_USERNAME/kraken-docker" .
docker push $DOCKER_USERNAME/kraken-docker

Running Kraken containers on the cluster nodes

Download Kraken Database

First we need to download the Kraken database to each of the hosts. We can use the SGE to distribute the jobs on the cluster. The -pe option ensures, that we only download the database once on each host:

qsub -N DB_Download -t 1-$NUM_NODES -pe multislot $NUM_CORES -cwd \
/vol/spool/docker-kraken-gcb/scripts/docker_run.sh \
$DOCKER_USERNAME/kraken-docker $HOST_SCRATCHDIR $HOST_SPOOLDIR \
/vol/scripts/kraken_download_db.sh

Run Kraken Analysis

Start the pipeline for just one input file:

qsub -N kraken_SRR935726 -pe multislot $NUM_CORES -cwd \
/vol/spool/docker-kraken-gcb/scripts/docker_run.sh \
$DOCKER_USERNAME/kraken-docker $HOST_SCRATCHDIR $HOST_SPOOLDIR \
"/vol/scripts/kraken_pipeline.sh SRR935726.fastq.gz SRR935726"

You will find the output files in /vol/spool.

If your pipeline is working, analyze all FASTQ files:

for i in `cat samples.txt | sed 's/.fastq.gz//g'`
do 
qsub -N kraken_$i -pe multislot $NUM_CORES -cwd \
/vol/spool/docker-kraken-gcb/scripts/docker_run.sh \
$DOCKER_USERNAME/kraken-docker $HOST_SCRATCHDIR $HOST_SPOOLDIR \
"/vol/scripts/kraken_pipeline.sh $i.fastq.gz $i"
done

Generate Krona plot

cd /vol/spool
for i in *out; do cut -f2,3 $i > $i.krona; done
ktImportTaxonomy *krona -o krona.html
cp -r krona.html* ~/public_html

You can use your browser to look at the Krona output. Go to: http://<BIBIGRID_MASTER>/~ubuntu/

Clean up

After logout, terminate the BiBiGrid cluster:

bibigrid -o bibigrid.properties -l
bibigrid -o bibigrid.properties -t CLUSTERID