GitHub Repos (IM)

As requested, a first-draft list or repositories that we currently use/intend to use for Diamond and Janssen work.

• Each has its own documentation that’s usually found in or referenced from the root README.md file.

• Documentation will obviously evolve as we progress and we are likely to create our own high-level ‘documentation’ repository to hold material that a) provides a more intuitive starting point and b) reduces duplication.

The repositories, all hosted in GitHub at Informatics Matters Ltd , each with a brief description, are: -

Fragnet Search

• fragnet.git - Fragment network tooling for our fragnet-search application

• fragnet-ui.git [PRIVATE] - A private repo for the fragnet-search user application, containing IP owned by Informatics Matters

• fragnet-ansible.git - Ansible playbooks and roles for the orchestration of the fragnet application

• docker-neo4j.git - A specialised image for the neo4j graph database, providing simpler and common fragnet database configuration

• docker-neo4j-ansible.git - Ansible playbooks and roles for the orchestration of our neo4j graph database

• ansible-graph-processor.git [PRIVATE] - Ansible playbooks, roles and workflows for the collection, fragmentation, augment and combination of graph databases, currently with an element of IP owned by Informatics matters

• ansible-bastion.git - Ansible playbooks and roles for the creation of cloud-based bastion machines

• ansible-galaxy-cloud.git - Ansible playbooks and roles for the creation and configuration of cloud-based fragment processing machines

• fragalysis.git [FORKED] - A fork of the xchem/fragalysis repository containing improvements to the fragment network build logic

Squonk

• squonk.git - The Squonk backend application including legacy orchestration playbooks for OpenShift

• squonk-ansible.git - Ansible playbooks and roles for Squonk orchestration (Kubernetes and Openshift)

• pipelines.git - Standard (public) Squonk pipelines

• pipelines-utils.git - Common utilities used by pipelines (published to PyPI) 

• pipelines-utils-rdkit.git - Utilities for RDKit-based pipelines (published to PyPI) 

• docker_nextflow.git - A Specialised nextflow image used by Squonk’s nextflow-based pielines

• docker-tej.git - A specialised tej images originally used for Tej-based pipeline job submission

Infrastructure

• ansible-infrastructure.git - Ansible playbooks and roles for the orchestration of application infrastructure components (databases, keycloak etc.)

• ansible-role-cert-manager.git - An Ansible role (published to Ansible Galaxy) for the deployment of the kubernetes certificate manager

• ansible-role-infrastructure-data.git - An Ansible role (published to Ansible Galaxy) for the management of infrastructure database resources

• ansible-role-infrastructure-user.git - An Ansible role (published to Ansible Galaxy) for the management of infrastructure keycloak users, roles and realms

• docker-sql-client.git - A lightweight container image for the execution of SQL commands, used by our infrastructure data role

Fragalysis

• dls-fragalysis-stack-openshift.git - Ansible playbooks and roles and anciliary data and images used by the existing (OpenShift) fragalysis stack deployment

• jenkins-utils.git - Utilities for the configuration of Jenkins, used by the existing (OpenShift) fragalysis stack deployment

• openshift-jenkins-buildah-slave.git - An OpenShift container image used by Jenkins to build fragalysis stack project images