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Last pushed: 2 years ago
Short Description
Docker image for JBrowse 1.12.0
Full Description

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/jbrowse-1.12.0

After this completes, JBrowse will be accessible from a web browser:
...
http://<server IP address>:8080
...

Example:

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
Docker Pull Command
Owner
jbrowse
Source Repository