dockstore-tool-bamstats

A repo for the Dockerfile to create a Docker image for the BAMStats command. Also contains the Dockstore.yml which is used by the Dockstore to register this container and describe how to call BAMStats for the community.

Building Manually

Normally you would let Quay.io build this. But, if you need to build manually you would execute:

docker build -t briandoconnor/dockstore-tool-bamstats:1.25 .

Running Manually

$ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
$ docker run -it -v `pwd`/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam:/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam briandoconnor/dockstore-tool-bamstats:1.25

# within the docker container
$ java -Xmx7g -jar /opt/BAMStats-1.25/BAMStats-1.25.jar -i /NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam -o test.html -v html

Running Through the Dockstore Descriptor Launcher

This tool can be found at the Dockstore Descriptor git repo. It lets you run a Docker container with a CWL descriptor locally, using Docker and the CWL command line utility. This is great for testing.

Create Config File

Call it launcher.ini:

working-directory=./datastore/

Make a Parameters JSON

This is the parameterization of the BAM stat tool:

{
  "bam_input": {
        "class": "File",
        "path": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam"
    },
    "bamstats_report": {
        "class": "File",
        "path": "s3://oicr.temp/testing-launcher/bamstats_report.zip"
    }
}

Run with Launcher

Run it using Java, make sure you have the dependencies installed for the Launcher, see the link above:

$ java -cp uber-io.github.collaboratory.launcher-1.0.2-SNAPSHOT.jar io.github.collaboratory.LauncherCWL --config launcher.ini --descriptor Dockstore.cwl --job sample_configs.json