Wellcome Trust Sanger Institute - Human Genetics Informatics
Analysing genomic data at scale for the Human Genetics Program
Cambridge, UK
Pinned Repositories
docker-proxify
Allows building and running docker container images from behind a corporate proxy
gatk-cwl-generator
Generates CWL files from the GATK documentation
go-softpack-builder
Go implementation of a softpack builder service
hail_analysis_pipelines
Hail based analysis pipelines for HG projects
ibackup
Performant backups of many files to iRODS
nextflow-pipelines
Nextflow HGI pipelines
openconnect-proxy
Provide an authenticated http proxy that provides connectivity via an OpenConnect VPN client (to connect to a compatible AnyConnect VPN server)
softpack-core
SoftPack Core
softpack-web
Softpack Web provides a graphical user interface for Softpack services.
yascp
scRNA multimodal analysis pipeline utilised for large dataset processing
Wellcome Trust Sanger Institute - Human Genetics Informatics's Repositories
wtsi-hgi/docker-proxify
Allows building and running docker container images from behind a corporate proxy
wtsi-hgi/gatk-cwl-generator
Generates CWL files from the GATK documentation
wtsi-hgi/ansible-style-guide
Style guide for writing Ansible
wtsi-hgi/arvados-pipelines
HGI arvados pipelines (crunch scripts, container Dockerfiles, pipeline templates, etc)
wtsi-hgi/gitlab-build-variables
Tools for managing GitLab CI pipeline build variables
wtsi-hgi/hgi-systems
Orchestration and configuration management of hgi systems (using terraform & ansible)
wtsi-hgi/mpistat
Efficiently lstat every file in a filesystem tree in parallel across multiple nodes using MPI.
wtsi-hgi/vareval
A collection of scripts for evaluating variant callers
wtsi-hgi/bindmapfuse
wtsi-hgi/ebi-ngs-workshop
HGI's materials for the EBI Next Generation Sequencing (NGS) workshop
wtsi-hgi/FPGA-Evaluation
A repository of scripts and other miscellaneous things for evaluating FPGA accelerated pipelines.
wtsi-hgi/hgi-registry
Human Genetics Programme project and team group registry API
wtsi-hgi/ansible-aptly-modules
Ansible modules for managing Aptly
wtsi-hgi/ansible-postgres-s3-backup
An Ansible role to backup Postgres to S3
wtsi-hgi/arvados
an open source platform for managing and analyzing biomedical big data
wtsi-hgi/common-workflow-language
Repository for the CWL standards. Use https://www.biostars.org/t/cwl/ for support 😊
wtsi-hgi/cromwell-setup
Our test setup for Cromwell on (and off) Google Cloud
wtsi-hgi/cwl-dummy
Generates CWL files that do nothing.
wtsi-hgi/cwl-scheduler-tests
wtsi-hgi/cwl-v1.1
In development version of the future CWL v1.1 specification
wtsi-hgi/docker-with-gitlab-secrets
Wraps Docker to run with GitLab build variables
wtsi-hgi/fs-reporting
wtsi-hgi/gatk-1
Official code repository for GATK versions 4 and up
wtsi-hgi/hgi-arvados-build
wtsi-hgi/hgi-jupyter-notebook
HGI's prebaked Jupyter notebook stack
wtsi-hgi/hgi-k8s
wtsi-hgi/hgi-registry-frontend
Client for the HGI Registry API
wtsi-hgi/hgi-software-builder
wtsi-hgi/python-cwlgen
Generation of CWL programmatically. Available types: CommandLineTool and DockerRequirement
wtsi-hgi/thrifty-builder
Builds Docker images, capturing information to reduce the frequency of future re-builds