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/ep_sotauth
Etherpad Lite plugin to trust authentication passed in from X-Forwarded-User HTTP header. This is useful when running behind a reverse proxy (a "series of tubes") that handles authentication. Do not use this plugin unless you have protected the server so that it can only be accessed from the reverse proxy.
wtsi-hgi/lustre_operator
Wrapper script to allow non-root users to run privileged lfs commands on particular Lustre filesystems (using sudo)
wtsi-hgi/olly-maersk
Containerisation-agnostic LSF execution configuration for Cromwell
wtsi-hgi/vr-runner
Runner pipelines
wtsi-hgi/arboretum
Tool to automate Branchserve instance management on OpenStack
wtsi-hgi/asclepius
Utility to apply metadata to iRODS objects
wtsi-hgi/branchserve
Treeserve/Lustretree meta repository with Docker scripts to easily launch and deploy Treeserve and its interface
wtsi-hgi/cromwell-pipelines
Cromwell pipelines for human genetic data
wtsi-hgi/cwltool
Common Workflow Language reference implementation
wtsi-hgi/fce_provisioning
A repository to set up an isolated FCE instance for researchers
wtsi-hgi/hgi-reports
Various reports for compute and storage usage.
wtsi-hgi/imirror
Copy a directory to iRODS and distribute the work over an LSF cluster
wtsi-hgi/irods-to-s3
iRODS to S3 copy tool
wtsi-hgi/JACKS
Analysis package for processing counts from genome-wide CRISPR/Cas9 screens
wtsi-hgi/krb-utils
Kerberos keytab utilities
wtsi-hgi/leafcutter_container
wtsi-hgi/login-page-swarm
Login Page For Swarm
wtsi-hgi/ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
wtsi-hgi/nf_cell_cell_interaction
Single Cell Nextflow cell cell interaction pipeline.
wtsi-hgi/nf_scrna_sccaf
wtsi-hgi/nginx-ldap-auth-original
LDAP Auth for swarm
wtsi-hgi/nginx-ldap-auth-swarm
wtsi-hgi/pcp
Parallel copy tool
wtsi-hgi/qadpg
Quick-and-Dirty PostgreSQL
wtsi-hgi/saige_jupyter
wtsi-hgi/sapling
Ansible playbook for quickly starting instances of Treeserve
wtsi-hgi/singularity-baton
baton, contained
wtsi-hgi/symlink-fixer
wtsi-hgi/warden
A web frontend for Arboretum
wtsi-hgi/wham-bam-thank-you-cram