GMOD/jbrowse-docker

Name: jbrowse-docker

Owner: Generic Model Organism Database Project

Description: JBrowse docker project

Created: 2016-09-08 00:36:30.0

Updated: 2018-02-21 15:29:42.0

Pushed: 2017-05-03 03:07:01.0

Homepage: null

Size: 600

Language: Shell

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README

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).

cker 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:

er-machine ip

Find the container ip address on linux/mac:

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

From a web browser:

://<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).

cker 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:

cker-compose up

Mount point

Data can be provided to the container via a mount:

cker 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:

rf $JBROWSE_DATA/json/yeast/;
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;

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

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

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

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