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
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
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>
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.
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 $DOCKER_USERNAME
Now every time you made a changes to the container scripts, you need to push the image to DockerHub:
docker build -t "$DOCKER_USERNAME/kraken-docker" .
docker push $DOCKER_USERNAME/kraken-docker
First we need to download the Kraken database to each of
the hosts. We can use the SGE to distribute the jobs on the
cluster. The -pe option ensures, that we only download the
database once on each host:
qsub -N DB_Download -t 1-$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
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
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/
After logout, terminate the BiBiGrid cluster:
bibigrid -o bibigrid.properties -l
bibigrid -o bibigrid.properties -t CLUSTERID