CancerCollaboratory/dockstore-tool-bamstats

Name: dockstore-tool-bamstats

Owner: CancerCollaboratory

Description: A repo for the BAMStats command, used as the tutorial for Dockstore

Created: 2015-10-25 20:18:18.0

Updated: 2017-08-07 15:28:13.0

Pushed: 2017-05-16 18:03:12.0

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Size: 98765

Language: Shell

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README

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.

Validation

This tool has been validated as a CWL draft-3 and v1.0 CommandLineTool.

Versions that we tested with are the following

 (1.8.1)
runner (1.0)
upgrader (0.1.1)
ool (1.0.20160712154127)
ma-salad (1.14.20160708181155)
ptools (25.1.6)

Building Manually

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

docker build -t collaboratory/dockstore-tool-bamstats:1.25-3 .

Running Manually

et ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
cker run -it -v `pwd`/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam:/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam collaboratory/dockstore-tool-bamstats:1.25-3

thin the docker container
sr/local/bin/bamstats 4 /NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam

You'll then see a file, bamstats_report.zip, in the current directory, that's the report file. You can use -v to mount the result out of the container.

Running Through the Dockstore CLI

This tool can be found at the Dockstore, login with your GitHub account and follow the directions to setup the CLI. 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.

Make a Parameters JSON

This is the parameterization of the BAM stat tool, a copy is present in this repo called sample_configs.json:

am_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": "/tmp/bamstats_report.zip"
}

Run with the CLI

Run it using the dockstore CLI:

e:
tch CWL
ockstore tool cwl --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-3 > Dockstore.cwl
ke a runtime JSON template and edit it (or use the content of sample_configs.json above)
ockstore tool convert cwl2json --cwl Dockstore.cwl > Dockstore.json
n it locally with the Dockstore CLI
ockstore tool launch --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-3 --json Dockstore.json