JBrowse

Configurable docker image for GMOD/JBrowse. http://jbrowse.org/

This docker image allows customization of loaded data; by placing executable shell scripts in the mounted folder, you can easily load data on boot.

Based On:

https://github.com/erasche/docker-jbrowse - Eric Rasche

Quick Start:

Run the docker image from linux shell (retrieves and installs if necessary).

$ docker run -p 8080:80 jbrowse/gmod-jbrowse

After this completes, JBrowse will be accessible from a web browser. Find the container ip address on windows:

docker-machine ip

Find the container ip address on linux/mac:

docker inspect --format '{{ .NetworkSettings.IPAddress }}' $(docker ps -q)

From a web browser:

http://<container IP address>:8080

running specific version:

(earliest docker image available is 1.12.0) Run the docker image from linux shell (retrieves and installs if necessary).

$ docker run -p 8080:80 jbrowse/gmod-jbrowse:1.12.0

Launching with YAML script:

A docker-compose.yml file is provided for your convenience, allowing you to boot up the example quite quickly:

$ docker-compose up

Mount point

Data can be provided to the container via a mount:

$ docker run -v `pwd`/my-data/:/data/ jbrowse/jbrowse-1.12.0

Startup Scripts

Running the default JBrowse instance is likely uninteresting, and you'd like to run it with your own data.

This is easy to do, just dump data in a folder and provide some .sh script(s) to load that data on boot. Here is an example of how the volvox data is loaded:

rm -rf $JBROWSE_DATA/json/yeast/;
bin/prepare-refseqs.pl \
    --fasta sample_data/raw/yeast_scaffolds/chr1.fa.gz \
    --fasta sample_data/raw/yeast_scaffolds/chr2.fa.gzip \
    --out $JBROWSE_DATA/json/yeast;

gunzip -c \
    $JBROWSE_DATA/yeast_scaffolds/chr1.fa.gz \
    $JBROWSE_DATA/raw/yeast_scaffolds/chr2.fa.gzip \
    > $JBROWSE_DATA/raw/yeast_chr1+2/yeast.fa;

bin/biodb-to-json.pl \
    --conf $JBROWSE_DATA/raw/yeast.json \
    --out $JBROWSE_DATA/json/yeast/;

bin/add-json.pl \
    '{ "dataset_id": "yeast" }' \
    $JBROWSE_DATA/json/yeast/trackList.json

bin/generate-names.pl --dir $JBROWSE_DATA/json/yeast/;

Environment Variables

There are a couple environment variables available to startup scripts:

Variable	Value/Use
`JBROWSE`	The location of the jbrowse installation, including the `index.html`
`JBROWSE_DATA`	Location for the `sample_data` folder which contains publicised data
`DATA_DIR`	Location of mounted data

enuggetry/docker-jbrowse