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Wellcome Trust Sanger Institute - Human Genetics Informatics

Login: wtsi-hgi

Company: null

Location: Cambridge, UK

email: hgi@sanger.ac.uk

Blog: http://www.sanger.ac.uk/

Members

Repositories

13amp: Userspace CRAM-to-BAM translation virtual filesystem
AdmixTools: Tools test whether admixture occurred and more
ansible: Ansible is a radically simple IT automation platform that makes your applications and systems easier to deploy. Avoid writing scripts or custom code to deploy and update your applications? automate in a language that approaches plain English, using SSH, with no agents to install on remote systems.
ansible-anaconda: Ansible role for installing Anaconda
ansible-conda: An Ansible module for managing Python packages via Conda
ansible-consul: Ansible role for consul
ansible-fluent-bit: Ansible role for Fluent Bit
ansible-fluentd: Ansible role : install and configure fluentd
ansible-logrotate: Ansible Galaxy role to setup logrotate and additional rotation scripts
ansible-module-infoblox: Awesome infobox module for ansible
ansible-postgres-s3-backup: An Ansible role to backup Postgres to S3
ansible-role-devstack: Install and setup Devstack
ansible-role-systemd-service: Register services to systemd.
ansible-style-guide: Style guide for writing Ansible
ansible-supergiant: Ansible role for configuring Supergiant
arvados: an open source platform for managing and analyzing biomedical big data
arvados-dev: Development tools for people who hack on arvados core
arvados-pipelines: HGI arvados pipelines (crunch scripts, container Dockerfiles, pipeline templates, etc)
async-test: Asynchronous testing decorator for Python projects
bam2cram-check: null
bamboo: HAProxy auto configuration and auto service discovery for Mesos Marathon
baton: iRODS client programs and API
bcftools: Human Genetics Informatics repository for bcftools (not official release)
bcviz: JavaScript visualisation for bamcheck file format
bdist: Submit a distributed job to your LSF compute cluster
beagle: Unofficial beagle 4.0/4.1 source code imported from http://faculty.washington.edu/browning/beagle/beagle.html
beamer-scaffold: Beamer presentation scaffold
bhaps: converters from text-based haplotype matrix to binary haplotype matrix, and for sampling haplotypes into genotypes
bissell: Dummy iRobot server for client testing
bloch: BLOCH project
boto: For the latest version of boto, see https://github.com/boto/boto3 -- Python interface to Amazon Web Services
bridgebuilder: BridgeBuilder efficiently remaps BAM/SAM reads to a new reference by first building a "bridge" reference, first mapping to that bridge, and then remapping only a subset of reads to the full new reference.
cache-analysis: null
cache-usage-simulator: null
capmq: Simple program to cap mapping quality in a given alignment file
chat-sharelatex: The ShareLaTeX backend chat API
clsi-sharelatex: A web api for compiling LaTeX documents in the cloud
clusterssh: Cluster SSH - Cluster Admin Via SSH
common-workflow-language: Repository for the CWL standards. Use https://www.biostars.org/t/cwl/ for support ?
composer: Visual and code editor for Common Workflow Language
consul-lock: CLI and Python interface for easily managing Consul locks
consul-template: Template rendering, notifier, and supervisor for @HashiCorp Consul and Vault data.
cookie-monster: COOKIES! Om nom nom nom...
cpython: The Python programming language
cronic: A cure for Cron's chronic email problem
cvmfs: The CernVM File System
cvmfs-test: A test framework for the CernVM-FS
cwl2nxf: Import a CWL workflow specification to Nextflow script (experimental)
cwltool: Common Workflow Language reference implementation
DNAOrderApp: Refining the process for ordering DNA Sequences
DNG_dev: HGI's current version of DenovoGear, not the official release. A program to detect denovo-variants using next-generation sequencing data. (http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html)
docker-arvados-client: An Arvados client/shell container image
docker-arvados-dev: Docker container for Arvados development (and running tests)
docker-baton: baton in a Docker container
docker-da: Docker image with with a Docker client and Ansible (DA)
docker-eigensoft: Dockerised EIGENSOFT software (https://github.com/DReichLab/EIG)
docker-elasticsearch: Ansible role for configuring Elasticsearch with Search Guard to run in Docker
dockerfile-arangodb: null
docker-gitlab-client: Docker image containing gitlab client from https://github.com/NARKOZ/gitlab
docker-icat: iRODS server in a Docker container
docker-kibana: Ansible role for configuring Kibana + Search Guard Plugin to run in Docker
docker-ok: null
docker-packer: Version of hashicorp/packer with openssl and without a custom entrypoint
docker-proxify: Allows building and running docker container images from behind a corporate proxy
docker-python-subrepo: Docker image with Python and Git Subrepo
docker-see-tree: Produces a diagram of the files in a given directory in a pdf
docker-texlive: Dockerfile to build a trusted build of a container including texlive
docker-ubuntu-python-pip: Trusted docker build based on ubuntu with addition of Python and pip
docker-with-gitlab-secrets: Wraps Docker to run with GitLab build variables
docstore-sharelatex: A CRUD API for storing and updating text documents in projects
document-updater-sharelatex: An API for applying incoming updates to documents in real-time
dstat: Versatile resource statistics tool
duplicity-backup.sh: Bash wrapper script for automated backups with duplicity supporting Amazon's S3 online storage as well as other storage destinations (ftp, rsync, sftp, local storage...).
ep_disable_lists: Etherpad Lite plugin to disable list/indentation controls.
ep_doi: Etherpad Lite plugin to enable doi: identifiers (linking automatically to http://dx.doi.org/)
ep_html_export_using_client_filters: Etherpad Lite plugin to allow use of client-side filters for HTML export (generates messier HTML, but allows plugins like ep_doi and ep_pubmed to work for HTML export)
ep_pubmed: Etherpad Lite plugin to enable pubmed: identifiers (linking automatically to http://ncbi.nlm.nih.gov/pubmed/)
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.
etherpad-lite: An Etherpad based on node.js - Our goal is to make collaborative editing the standard on the web
filestore-sharelatex: An API for CRUD operations on binary files stored in S3
flashpca: Fast Principal Component Analysis of Large-Scale Genome-Wide Data
flask: A microframework based on Werkzeug, Jinja2 and good intentions (unofficial fork)
flask-restful: Simple framework for creating REST APIs (unofficial fork)
FPGA-Evaluation: A repository of scripts and other miscellaneous things for evaluating FPGA accelerated pipelines.
freebayes: Bayesian haplotype-based polymorphism discovery and genotyping.
fs-reporting: null
fuse: FUSE library for Go.? go get bazil.org/fuse ?
gatk: GATK Official Release Repository: contains the core MIT-licensed GATK framework, free for all uses
gatk-cwl-generator: Generates CWL files from the GATK documentation
gatk-protected: GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only
GEMMA: Genome-wide Efficient Mixed Model Association
genetics-magic: null
GGR-cwl: CWL tools and workflows for GGR
git-common-sync: A tool to synchronise common files between Git repositories
github-to-gitlab-hook: Webhook to sync Github repos to internal Gitlab repos.
gitlab-build-variables: Tools for managing GitLab CI pipeline build variables
gitlab-ci-git-push: Gitlab CI runner image that pushes to a remote Git repo (Dokku, Heroku, Deis, etc.)
gitlab-runner-canary: null
glance-proxy: Proxy to provide image data from glance via HTTP, using an S3 temporary store to support Range requests
go-infoblox: Golang Infoblox WAPI Library
graph: Graph package providing various implementations of graph data structures and graph processing algorithms.
hail: Scalable genomic data analysis.
hapi-ur: HAPI-UR: HAPlotype Inference for UnRelated samples (cloned from: https://code.google.com/p/hapi-ur)
hattie: Control panel for HGI Users to Request work be done
henplus: HenPlus is a SQL shell that can handle multiple sessions in parallel. The commandline interface with the usual history functions features TAB-completion for commands, tables and columns. Database connect via JDBC.
hgc-deploy: Tools for creating and running Mercury containers. (now deprecated in favour of hgc-tools)
hgc-tools: Set of tools for working with Mercury capsules.
hgi-arvados-openstack: null
hgi-bamcheck-frontend: null
hgi-bamcheck-server: Serves bamcheck files from vrpipe via http
hgi-cookie-monster: CookieMonster setup for HGI
hgi-docker-registry: HGI flavour of docker registry Dockerfile
hgi-groups: Human Genetics Programme group registry
hgi-groups: Human Genetics Programme group registry
hgi-image-creation: Builds on ISG's image-creation to allow provisioning images using entire ansible playbooks remotely
hgi-project: HGI Project tracking database
hgi-qc-frontend: Web frontend for qc data
hgi-groups: Human Genetics Programme group registry
hgi-groups: Human Genetics Programme group registry
hgi-reports: Various reports for compute and storage usage.
hgi-rt: RT customisations for HGI
hgi-scripts: null
hgi-systems: Orchestration and configuration management of hgi systems (using terraform & ansible)
hgi-vrtrack-qc-server: Serves QC data from vrtrack database via http.
hgi-web: null
hgi-web_apitoken: Issue API access tokens to otherwise authenticated clients
hgi-web_usermod: User roles authentication module for HGI-web
hgquota: Tools for Sanger humgen users to find out information about available disk quota.
htslib: C library for high-throughput sequencing data formats
htslib-plugins: Plugins for use with HTSlib
hts-specs: SAM/BAM specification
https-everywhere: A browser extension that encrypts your communications with many websites that offer HTTPS but don't yet enforce it.
http-status-puppet: A HTTP server that will return a status code of your choice
illumina2bam: Generate and process BAM files from Illumina sequencing instrument files
iquestFuse: iquest-like iRODS FUSE client (allows navigation of metadata via a virtual POSIX filesystem)
irobot: iRODS data brokerage service
irobot-client: Basic client to interact with the iRobot HTTP API.
irods: Middleware for your critical data.
irodsa-utilities: Convenience scripts for reading/creating the contents of .irodsA files
iRODS-Solr: Offload irods metadata querying to an apache solr instance
IYG: Inside Your Genome Project
IYG-Import: Python Data Importer for IYG Web
IYG-SOT-Web: SNP and Trait description crowdsourcing site for the Inside Your Genome project.
IYG-SOT-Web-Lib: Inside Your Genome Trait and SNP description Crowdsourcing Site Perl Modules
IYG-Web: "Inside Your Genome" Web App
IYG-Web-Lib: Perl Library for IYG Web
jinjath: Jinja Template Helpers
jquery-dynatable: A more-fun, semantic, alternative to datatables
json: JSON for Modern C++
jsql: Java program to allow connecting to any database to run select queries, and outputting the results in various formats. Mainly used to return data from sql queries in a form that can be easily eval'd in python.
kaiwa: A modern XMPP Web client
keep-cache-testing: null
klib: A standalone and lightweight C library
ldapvi: Clone of ldapvi from http://www.lichteblau.com/git/ldapvi.git
lmdb-test: null
lofi: Sequence alignment data downsampling tool
logger-sharelatex: A module encapsulating standard logging features for ShareLaTeX services
lustre_changelog_dummy: Dummy program to test lustre changelogs
lustre_operator: Wrapper script to allow non-root users to run privileged lfs commands on particular Lustre filesystems (using sudo)
marathon-client.py: null
mattermost-integration-gitlab: Send events from Gitlab to Mattermost through webhooks
mercury: Overarching repository for work on Mercury.
metacarpa: Fork of https://bitbucket.org/agilly/metacarpa
metadata-check: Tests to perform on the iRODS metadata for a BAM file, versus the information in the file header
metrics-sharelatex: A drop-in metrics and monitoring module for node.js apps
minio-go: Minio Go Library for Amazon S3 compatible cloud storage
mkfs_udf_portable_hd: Perl utility to format UDF hard drive on Linux for portable use across Linux, Mac, and Windows
mod-proxy-add-user: a tiny apache module to pass REMOTE_USER via headers to proxy servers
modules: Fork of http://modules.sourceforge.net/ (this version has been modified primarily to add more complete bash completion as well as tcsh completion)
mpistat: Efficiently lstat every file in a filesystem tree in parallel across multiple nodes using MPI.
ncbi-vdb: ncbi-vdb
netlib-java: null
node-http-write: Raw HTTP response writer with basic templating
nodervisor: Supervisor manager in node.js
openconnect-proxy: Provide an authenticated http proxy that provides connectivity via an OpenConnect VPN client (to connect to a compatible AnyConnect VPN server)
openstack-info: Gets information about what is in an OpenStack tenant
openstack-tenant-cleaner: Cleans up old images, instances and keys in OpenStack tenants based on a configuration
openstack-tools: null
packer: Packer is a tool for creating identical machine images for multiple platforms from a single source configuration.
pcp: Parallel copy tool
petardfs: PetardFS - a FUSE filessytem for injecting intentional errors (e.g. for testing)
picard: A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
pigpio-go: Go bindings for pigpio C library for Raspberry Pi GPIO
Platypus: Platypus Variant Caller
plink-ng: A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).
profiles: contributed profiles
proxygen: A collection of C++ HTTP libraries including an easy to use HTTP server.
python-baton-wrapper: Python 3 wrapper for baton
python-capturewrap: Wraps callables to capture stdout, stderr, exceptions and the return
python-common: [DEPRECATED] Python 3 common library
python-consul: Python client for Consul (http://www.consul.io/)
python-git-subrepo: Provides access to `git subrepo` in Python
python-hgijson: Python library for easily JSON encoding/decoding complex class-based Python models, using an arbitrarily complex (but easy to write!) mapping schema.
python-hgijson: Python library for easily JSON encoding/decoding complex class-based Python models, using an arbitrarily complex (but easy to write!) mapping schema.
python-hgijson: Python library for easily JSON encoding/decoding complex class-based Python models, using an arbitrarily complex (but easy to write!) mapping schema.
python-hgijson: Python library for easily JSON encoding/decoding complex class-based Python models, using an arbitrarily complex (but easy to write!) mapping schema.
python-rt: Clone of git://git.nic.cz/python-rt.git
python-sam-header-parser: null
python-sequencescape-db: Python 3 client for a Sequencescape database
python-simple-openstack: Python library for getting and manipulating items in OpenStack in a simple way
python-temp-helpers: Python library to help with using temp files and directories
python-test-helpers: Python library to help with creating tests
redis-sharelatex: a wrapper around redis which detects if it should use the normal redis driver or redis-sentinel
redsocks: transparent redirector of any TCP connection to proxy (unofficial copy)
rendr: Render your Backbone.js apps on the client and the server, using Node.js.
replace_reads: Replaces reads in a BAM file
rss: Regression with Summary Statistics
rt-integration: Fetches tickets from RT (using REST API) and sends them to webhook
r-travis: Tools for using R with Travis (http://travis-ci.org)
rt-subject-from-fields: Set subject of RT tickets based on field values (including custom fields)
runit: Unofficial fork of runit (official home: http://smarden.org/runit/)
s3cmd: Official s3cmd repo -- Command line tool for managing Amazon S3 and CloudFront services
samtools: Human Genetics Informatics repository for samtools (not official release)
secrets: A command line based secrets manager
seq_autoqc: Additional high-throughput sequencing autoQC steps
serapis: Serapis archival system
serapis-web: null
serf: Service orchestration and management tool.
settings-sharelatex: A small module to allow global config settings to be set for all services within the ShareLaTeX architecture.
shadowbroker: Quick tool to connect the HGI queues on RT to the MUC
sharelatex: A web-based collaborative LaTeX editor
smith-waterman-demo: Javascript demonstration of smith waterman alignment
spec: ALPS Specification documents.
spelling-sharelatex: The backend spellcheck API that performs spell checking for ShareLaTeX
ssh-keydgen: Generate Deterministic SSH keys
sso-devise-omniauth-provider: A devise Omniauth server which handles Single Sign On
stag: Stream Aggregator
supergiant: Automatically scale hardware and easily run stateful applications using Kubernetes.
supervisor: Supervisor process control system for UNIX
tabix: Note: tabix and bgzip binaries are now part of the HTSlib project.
tabula: Project logging and analysis in the console.
tags-sharelatex: An API for managing project tags/folders in ShareLaTeX
tarbomb-disposal: Extract a tar archive, defusing any tarbombs
tarchecksum: null
tardis: Toolkit for automated and rapid discovery of structural variants
tar-mtime-zero: null
tears: Stream files to and from iRODS
terraform: Terraform is a tool for building, changing, and combining infrastructure safely and efficiently.
terraform-provider-infoblox: Infoblox plugin for Terraform
terraform-provider-openstack: Terraform OpenStack provider
terragrunt: Terragrunt is a thin wrapper for Terraform that supports locking for Terraform state and enforces best practices.
test-with-baton: Simplifying the testing of software that uses baton
test-with-irods: Deprecated: Use https://github.com/wtsi-hgi/useintest/ instead
thrifty-builder: null
track-changes-sharelatex: An API for saving and compressing individual document updates into a browsable history
translate_header: null
translations-sharelatex: holds the translations used for ShareLaTeX.com
treeserve: null
triple-e: Docker and Docker Machine wrapper scripts for OS X
update_pipeline: null
useintest: I don't care how it's done, I just want to use it in my tests!
vareval: A collection of scripts for evaluating variant callers
vcftools: A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
VerifyBamID: A Robust tool for estimation of DNA contamination and genetic ancestry from sequence reads
verifyBamID-1: null
vg: tools for working with variant graphs
vr-codebase: The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute (HGI edition)
vr-pipe: Generic pipeline system
vr-runner: Runner pipelines
wdl2cwl: Convert Workflow Definiton Language (WDL) to CWL
webhook-router: A system that accepts incoming webhooks from the Internet and routes them to internal locations, depending on a configuration that can be dynamically modified by users
web-sharelatex: The web front end for ShareLaTeX, a web-based collaborative LaTeX editor
werkzeug: A flexible WSGI implementation and toolkit (unofficial fork)
wings: WINGS Workflow System
www-hierarchical-fairshare: Tools to view LSF hierarchical fairshare UserGroup shares and current priority (e.g. in a treemap)
xadder: Open source tool for working with XAD files
xiongxiong: Bearer token codec
XKCD-password-generator: Generate secure multiword passwords/passphrases, inspired by XKCD
yaosadis: Yet Another OpenStack Ansible Dynamic Inventory Script
yatadis: Yet Another Terraform Ansible Dynamic Inventory Script (yatadis)
yggdrasil: Node.js framework for hypr-based graph information systems
ypip: Recursive pip for VCS-based packages

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.