kclem/dockstore-tool-bamstats repository overview
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
avro (1.8.1)
cwl-runner (1.0)
cwl-upgrader (0.1.1)
cwltool (1.0.20160712154127)
schema-salad (1.14.20160708181155)
setuptools (25.1.6)
Tested on Dockstore version 1.0-rc.2
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
$ 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 collaboratory/dockstore-tool-bamstats:1.25-3
# within the docker container
$ /usr/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:
{
"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": "/tmp/bamstats_report.zip"
}
}
Run with the CLI
Run it using the dockstore CLI:
Usage:
# fetch CWL
$> dockstore tool cwl --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-3 > Dockstore.cwl
# make a runtime JSON template and edit it (or use the content of sample_configs.json above)
$> dockstore tool convert cwl2json --cwl Dockstore.cwl > Dockstore.json
# run it locally with the Dockstore CLI
$> dockstore tool launch --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-3 --json Dockstore.json
Tag summary
Content type
Image
Digest
Size
171.6 MB
Last updated
over 7 years ago
docker pull kclem/dockstore-tool-bamstats