bioinformaticsua/catalogue repository overview

⁠Catalogue - Fingerprint Browser, deployment with docker

This repository is a Dockerfile for Catalogue, Fingerprint Browser. The original repository of Catalogue is located: https://github.com/bioinformatics-ua/catalogue⁠

This contains docker file for:

• Stable version (master)
• Development version (dev)

⁠How to run Catalogue?

Dependencies:

• docker (https://docs.docker.com/⁠)
• docker-compose: https://docs.docker.com/compose/⁠.

⁠Run

Note: you need to go to master or dev directory.

git clone https://github.com/bioinformatics-ua/catalogue-docker.git -b dev
cd master (or dev)
sh run.sh

Go to: 127.0.0.1:80/catalogue_dev/

⁠User and password (default)

Username: demo

Password: catalogue

⁠Aproval account

Add the following content to local_settings.py. This is important because this users will approve new registrations.

This is a dummy example, please change for the contacts of your organization.

ADMINS = (
    ('Luis A. Bastiao Silva', '[email protected]'),
    ('José Luis Oliveira', '[email protected]'),
    ('Ricardo Ribeiro', '[email protected]'),
)

⁠Email configurations

Add the following content to docker-compose.yml:

EMAIL_HOST = 'smtp.yourserver.org'
EMAIL_HOST_PASSWORD = 'passwordHERE'
EMAIL_HOST_USER = '[email protected]'
EMAIL_PORT = 25
EMAIL_USE_TLS = True
DEFAULT_FROM_EMAIL = "[email protected]"

⁠Configure ports, address, or persistence

Please, consider edit docker-compose.yml.

For persistance, things like that can be added in all volumes.

- ../persistence_dev/postgres:/data

For change expose ports (left side is the external, the right side, you do not change) - follow the example, of mapping the 80 to 8080:

ports:
    - "8080:80"

For change the URL where it will run:

- PUBLIC_IP=192.168.10.10:3000 # the public ip must be specified, to prevent fake HTTP Host headers
- BASE_DIR=catalogue

It will run in: http://192.168.10.10:3000/catalogue⁠

⁠Build your own container

Note: you need to go to master or dev directory.

You have to choose one and try to create a Docker container with the following command:

sh build

⁠Do you want to stop the docker container?

docker-compose stop

⁠Are you a developer?

Please, if you are a developer and you want to use a Docker for developing, consider to build your own image.

Nevertheless, it is possible to share your code, only editing docker-compose.yml. Add it in catalogue, near by image.

volumes:
    - /Users/your_user/Documents/catalogue:/project/catalogue

⁠Are you using Mac OS X or Windows?

⁠Windows

If you are in Windows, please consider to install docker-compose inside boot2docker.

Jump to virtual machhine with:

boot2docker ssh

Install docker-compose:

wget -P /tmp/ http://www.tinycorelinux.net/5.x/x86/tcz/python.tcz && tce-load -i /tmp/python.tcz && rm -f /tmp/python.tcz
curl -LO -k https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py && sudo /usr/local/bin/python2.7 ez_setup.py && rm -f ez_setup.py
sudo /usr/local/bin/easy_install-2.7 pip
sudo /usr/local/bin/pip2.7 install -U docker-compose==1.2.0

⁠Mac OS

Please consider to install Kitematic: https://kitematic.com/⁠

⁠Mantainers

• Luís A. Bastião Silva [email protected]⁠
• Ricardo Ribeiro [email protected]⁠

⁠Contact

• José Luis Oliveira [email protected]⁠