wtsi-hgi/ep_sotauth

This repository has been archived on 26/Nov/2019
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Created about 12 years ago
Updated about 5 years ago

wtsi-hgi/ep_sotauth

wtsi-hgi

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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.

docker-proxify

Allows building and running docker container images from behind a corporate proxy

openconnect-proxy

Provide an authenticated http proxy that provides connectivity via an OpenConnect VPN client (to connect to a compatible AnyConnect VPN server)

gatk-cwl-generator

Generates CWL files from the GATK documentation

yascp

scRNA analysis pipeline

eqtl

nextflow-pipelines

Nextflow HGI pipelines

ansible-style-guide

Style guide for writing Ansible

bsub_jupyter_lab

start jupyterlab python and R server on LSF farm5 node via bsub

python-hgijson

Python library for easily JSON encoding/decoding complex class-based Python models, using an arbitrarily complex (but easy to write!) mapping schema.

consul-lock

CLI and Python interface for easily managing Consul locks

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.

hgi-systems

Orchestration and configuration management of hgi systems (using terraform & ansible)

arvados-pipelines

HGI arvados pipelines (crunch scripts, container Dockerfiles, pipeline templates, etc)

serapis

Serapis archival system

rstudio_sanger_lsf_farm

bsub Rstudio server on Sanger LSF farm, with access to /lustre, to be accessed via web browser

mpistat

Efficiently lstat every file in a filesystem tree in parallel across multiple nodes using MPI.

single_cell_annotation

gitlab-build-variables

Tools for managing GitLab CI pipeline build variables

bam2cram-check

hgi-web

IYG

Inside Your Genome Project

13amp

Userspace CRAM-to-BAM translation virtual filesystem

treeserve

vareval

A collection of scripts for evaluating variant callers

Common Workflow Language

ldapvi

Clone of ldapvi from http://www.lichteblau.com/git/ldapvi.git

metadata-check

Tests to perform on the iRODS metadata for a BAM file, versus the information in the file header

nf_scrna_qc

Single cell RNA-seq quality control, transcription profile clustering & cell-type assignment

lustre_operator

Wrapper script to allow non-root users to run privileged lfs commands on particular Lustre filesystems (using sudo)

yatadis

Yet Another Terraform Ansible Dynamic Inventory Script (yatadis)

hapi-ur

HAPI-UR: HAPlotype Inference for UnRelated samples (cloned from: https://code.google.com/p/hapi-ur)

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

seq_autoqc

Additional high-throughput sequencing autoQC steps

docker-icat

iRODS server in a Docker container

www-hierarchical-fairshare

Tools to view LSF hierarchical fairshare UserGroup shares and current priority (e.g. in a treemap)

nf_scrna_deconvolution

CellSNP-Vireo deconvolution pipeline, with optional genotype input.

mercuryrc

ebi-ngs-workshop

HGI's materials for the EBI Next Generation Sequencing (NGS) workshop

helpful-genestack-scripts

Some useful scripts for use with genestack

single_cell

Single Cell pipelines used at Sanger

irodsa-utilities

Convenience scripts for reading/creating the contents of .irodsA files

cwl-graph-generate

Generates https://view.commonwl.org/ like workflows images, showing a complete workflow.

serapis-web

hgi-vault

Data retention policy tools

SSDV

nf_cellbender

Single cell Nextflow cellbender pipeline.

yggdrasil

Node.js framework for hypr-based graph information systems

hail_analysis_pipelines

Hail based analysis pipelines for HG projects

ansible-fluent-bit

Ansible role for Fluent Bit

bindmapfuse

docker-baton

baton in a Docker container

coloc

tarbomb-disposal

Extract a tar archive, defusing any tarbombs

secrets

A command line based secrets manager

indelible-docker

docker image instructions for Indelible

genestack-uploader

A HTTP server providing an API and a frontend for easy uploading to Genestack

openstack-info

Gets information about what is in an OpenStack tenant

cookie-monster

COOKIES! Om nom nom nom...

shadowbroker

Quick tool to connect the HGI queues on RT to the MUC

FPGA-Evaluation

A repository of scripts and other miscellaneous things for evaluating FPGA accelerated pipelines.

python-capturewrap

Wraps callables to capture stdout, stderr, exceptions and the return

docker-cookhla

python-rt

Clone of git://git.nic.cz/python-rt.git

github-to-gitlab-hook

Service to sync GitHub and GitLab repositories

hgi-registry

Human Genetics Programme project and team group registry API

hgi-cloud

terraform and ansible codebase to provision clusters (e.g. hail/spark) at Sanger