A fresh software build

REBUILDING A SERVER WILL DELETE ALL CURRENT DATA ON THE SERVER.

To set up the server with a fresh build, you first need to return it to it's original state. Ask Volac I.T. to wipe the server and install ubuntu-20.04 and java, openjdk-11.

Next, use an ansible playbook to set up necessary software tools. This is automated by an ansible playbook, vg-install. Follow the install instructions on the playbook's website.

The playbook has been tested using GitHub Actions.

Info

The playbook will set up the server with the original software versions.

As well as installing the necessary software, the ansible playbook sets up the genome_tools/ folder and populates it with Tool 1, Tool 2 and Tool 3.

Tool 4, the Core, and the maintenance and reference libraries folders need to be added manually, see below.

Populating the new build

Four modules are not set up automatically by the ansible playbook. They are stored in private repositories in the volac-genomics GitHub site. They can be cloned to the local server as follows.

1. Authenticate to GitHub

Using the command line, enter the following commands substituting your details for Fred's:

git config --global user.name Fred Blogs

git config --global user.email fred.blogs@place.com

ssh -T git@github.com

Next, follow these instructions to create a personal access token. You will need this to access GitHub.

2. Clone the repositories

Using the command line, change directory using:

cd ~/genome_tools/

Then enter the following commands to clone the private repositories to your local server. You will need to enter your personal access token each time. The token starts ghp_.

git clone https://github.com/volac-genomics/Core.git

git clone https://github.com/volac-genomics/Tool_4.git

git clone https://github.com/volac-genomics/reference_libraries.git

git clone https://github.com/volac-genomics/maintenance.git

The server has now been restored to it's original state.