Here you can find a set of containers to help creating a bioinformatics core architecture, for example:

• LDAP server
• PostgreSQL server
• NFS server (Not active)
• Samba server (for integration with sequencer technology like Illumina)
• Galaxy server
• Zabbix server
• Software server (i.e. a lot of pre-installed software)
• Interative Compute server (a place for users to login)
• SLURM head node
• SLURM node

We use Alpine Linux for simple servers (very small footprint) and Ubuntu for larger images. It might happen that some containers are derived from Debian ones.

Todo: script to create docker volume directory structure

• Python 3.5+
• PyYAML
• Docker
• Ansible (including playbook)
• docker-py

If you use the setup wizard

• Flask
• openssl and pyOpenSSL (if you need to generate keys)

(explain with conda)

This will install all your servers on the local machine. If you have a very large big-iron machine, this might be what you want. If you have a cluster, this is still a reasonable starting point, though you will have some work to do, especially on the security front.

1. Use the wizard to configure the most complicated stuff: PYTHONPATH=. python -m wizard

2. Create a directory that will store all your docker volumes. This might need to be very big.

3. python3 src/prepare_templates.py [Directory_Above] . Prepares the ansible templates (this probably can be put inside ansible).

4. Optional and not recommended: python3 src/use_examples.py . This will copy the example configuration files to be used as the default ones. Make sure to change things in your final configuaration. You only run this if you did not run step 1, the wizard. Suggestion: run the wizard.

4. python3 src/create_directory_structure.py [Directory_Above]
5. cp etc/host.sample etc/hosts
6. cd ansible; ansible-playbook --ask-pass -i ../etc/hosts main.yml

The sequencer Samba file configuration was originally inspired on David Personette's Samba container. It is currently completely different.

The current Galaxy configuration is based on Björn Grüning's Galaxy container.

Copyright by Tiago Antao. Licensed under GNU Affero General Public License version 3.