GitHub Repos (IM)

Owned by Skyner, Rachael (DLSLtd,RAL,LSCI) (Unlicensed)
Feb 04, 2020
2 min read

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