/docker-jbrowse

Docker recipe for JBrowse (web-based genome browser)

MIT LicenseMIT

docker-jbrowse

Docker recipe for JBrowse

Instructions

Building & Running

docker build .
docker run --publish 8080:80 --volume $PWD/my-data:/data <image id>

Importing Data

(example using Bacterial genome annotated using RAST)

# connect to running Docker container:

docker exec -t -i <container id> /bin/bash

# now, from the container

# import reference:
bin/prepare-refseqs.pl --fasta /data/reference.fasta

# import features (GFF)
bin/flatfile-to-json.pl \
  --gff /data/annotation.gff \
  --trackType CanvasFeatures \
  --trackLabel "RAST Annotation"
  
# import assembly (SAM)
# (TODO)

# disconnect from container
exit

You should be able to browse your genome by pointing your browser to: http://dockerhost:8080/jbrowse/.

You can now commit the container with your data so that it will already be there the next time you start it up:

docker commit <container id>
docker tag <container id> my-genome-jbrowse

The next time you want to start JBrowse with your data:

docker start my-genome-jbrowse