Docker recipe for JBrowse
docker build .
docker run --publish 8080:80 --volume $PWD/my-data:/data <image id>
(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