DolphinNext docker version (CECAD)

DolphinNext original repository is located at https://github.com/UMMS-Biocore/dolphinnext.

This Docker configuration is based on https://github.com/UMMS-Biocore/dolphinnext-docker and https://github.com/UMMS-Biocore/dolphinnext-studio

For the Dolphinnext quick start guide please check: https://dolphinnext.readthedocs.io/en/latest/dolphinNext/quick.html

DolphinNext can be run as a standalone application using a docker container. First docker image need to be build, any change in the Dockerfile requires the image to be built.

Build docker image

1. To build docker image first clone one of the latest dolphinnext-docker

git clone https://github.com/CECADBioinformaticsCoreFacility/dolphinnext-docker.git

2. Build the image

cd dolphinnext-docker
docker build -t dolphinnext-docker .

Start the container

1. We move database outside of the container to be able to keep the changes in the database everytime you start the container.

N.B. The database files in /export will need to be backed up regularly

Please choose a directory in your machine to mount and replace /path/to/mount with your path.

• Note: Please don't change the target directory(/export) in the docker image.

mkdir -p /path/to/mount

2. While running the container;

docker run --name=CECAD-dolphinnext -m 10G -p 8080:80 -v /path/to/mount:/export -dti dolphinnext-docker

3. After you start the container, you need to connect to it and start the mysql and apache server usign the command below:

docker exec CECAD-dolphinnext /bin/bash

Once connected run the startup script located at bin/startup in this repository

startup

Disconnect from the container leaving it running the background

exit

4. Verify that dolphinnext and mysql folders are located inside of the export folder:

ls /export

5. Now, you can open your browser to access dolphinnext using the url below.

http://localhost:8080/dolphinnext

Hosting settings

We define localhost:8080 in /path/to/mount/dolphinnext/config/.sec file and use that to log in or other operations.

See the example file example_.sec_file.txt

You need to change localhost to the IP address or domain you use. Please update BASE_PATH and PUBWEB_URL as follows:

BASE_PATH = http://localhost:8080/dolphinnext
PUBWEB_URL = http://localhost:8080/dolphinnext/tmp/pub

to

BASE_PATH = http://your_temporary_domain_name:8080/dolphinnext
PUBWEB_URL = http://your_temporary_domain_name:8080/dolphinnext/tmp/pub

• Please don’t change other lines because others are used inside of docker.