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.
https://github.com/erasche/docker-jbrowse - Eric Rasche
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
(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
A docker-compose.yml
file is provided for your convenience, allowing you to boot up the example quite quickly:
$ docker-compose up
Data can be provided to the container via a mount:
$ docker run -v `pwd`/my-data/:/data/ jbrowse/jbrowse-1.12.0
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/;
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 |