<commit_before>------------------------------------------------
A Bioinformatics core based on Docker containers
------------------------------------------------

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

Base images
-----------

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

Dependencies
------------

- 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)


Installation
------------


TODO: refer the easy to use web configuration interface!

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.

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

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

3. ``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.

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``<commit_msg>Author and license<commit_after>------------------------------------------------
A Bioinformatics core based on Docker containers
------------------------------------------------

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

Base images
-----------

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

Dependencies
------------

- 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)


Installation
------------


TODO: refer the easy to use web configuration interface!

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.

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

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

3. ``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.

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``


Author and License
------------------

Copyright by <NAME>. Licensed under GNU Affero General Public License
version 3.

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