Wellcome Trust Sanger Institute - Human Genetics Informatics (@wtsi-hgi)
Guthub

wtsi-hgi

Twitter logo Share LinkedIn logo Share Facebook logo Share

Top repositories

1

docker-proxify

Allows building and running docker container images from behind a corporate proxy
Perl
83
star
2

openconnect-proxy

Provide an authenticated http proxy that provides connectivity via an OpenConnect VPN client (to connect to a compatible AnyConnect VPN server)
Shell
10
star
3

gatk-cwl-generator

Generates CWL files from the GATK documentation
Python
7
star
4

yascp

scRNA analysis pipeline
Python
7
star
5

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.
JavaScript
5
star
6

eqtl

Python
4
star
7

nextflow-pipelines

Nextflow HGI pipelines
Nextflow
4
star
8

ansible-style-guide

Style guide for writing Ansible
4
star
9

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
4
star
10

bsub_jupyter_lab

start jupyterlab python and R server on LSF farm5 node via bsub
Python
4
star
11

consul-lock

CLI and Python interface for easily managing Consul locks
Python
4
star
12

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.
Shell
4
star
13

hgi-systems

Orchestration and configuration management of hgi systems (using terraform & ansible)
HCL
3
star
14

arvados-pipelines

HGI arvados pipelines (crunch scripts, container Dockerfiles, pipeline templates, etc)
Python
3
star
15

serapis

Serapis archival system
Python
3
star
16

rstudio_sanger_lsf_farm

bsub Rstudio server on Sanger LSF farm, with access to /lustre, to be accessed via web browser
Shell
3
star
17

mpistat

Efficiently lstat every file in a filesystem tree in parallel across multiple nodes using MPI.
Python
3
star
18

single_cell_annotation

Python
3
star
19

gitlab-build-variables

Tools for managing GitLab CI pipeline build variables
Python
3
star
20

bam2cram-check

Python
3
star
21

hgi-web

JavaScript
2
star
22

nf_scrna_qc

Single cell RNA-seq quality control, transcription profile clustering & cell-type assignment
Python
2
star
23

IYG

Inside Your Genome Project
JavaScript
2
star
24

13amp

Userspace CRAM-to-BAM translation virtual filesystem
C
2
star
25

treeserve

C++
2
star
26

vareval

A collection of scripts for evaluating variant callers
Common Workflow Language
2
star
27

ldapvi

Clone of ldapvi from http://www.lichteblau.com/git/ldapvi.git
C
2
star
28

metadata-check

Tests to perform on the iRODS metadata for a BAM file, versus the information in the file header
Python
2
star
29

lustre_operator

Wrapper script to allow non-root users to run privileged lfs commands on particular Lustre filesystems (using sudo)
Perl
2
star
30

yatadis

Yet Another Terraform Ansible Dynamic Inventory Script (yatadis)
Python
2
star
31

hapi-ur

HAPI-UR: HAPlotype Inference for UnRelated samples (cloned from: https://code.google.com/p/hapi-ur)
C++
2
star
32

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
Vue
2
star
33

www-hierarchical-fairshare

Tools to view LSF hierarchical fairshare UserGroup shares and current priority (e.g. in a treemap)
Go
1
star
34

seq_autoqc

Additional high-throughput sequencing autoQC steps
R
1
star
35

nf_scrna_deconvolution

CellSNP-Vireo deconvolution pipeline, with optional genotype input.
Nextflow
1
star
36

mercuryrc

Shell
1
star
37

ebi-ngs-workshop

HGI's materials for the EBI Next Generation Sequencing (NGS) workshop
TeX
1
star
38

helpful-genestack-scripts

Some useful scripts for use with genestack
Shell
1
star
39

cwl-graph-generate

Generates https://view.commonwl.org/ like workflows images, showing a complete workflow.
Python
1
star
40

single_cell

Single Cell pipelines used at Sanger
Shell
1
star
41

irodsa-utilities

Convenience scripts for reading/creating the contents of .irodsA files
Python
1
star
42

hgi-vault

Data retention policy tools
Python
1
star
43

SSDV

JavaScript
1
star
44

nf_cellbender

Single cell Nextflow cellbender pipeline.
Python
1
star
45

yggdrasil

Node.js framework for hypr-based graph information systems
JavaScript
1
star
46

serapis-web

Python
1
star
47

docker-icat

iRODS server in a Docker container
Shell
1
star
48

hail_analysis_pipelines

Hail based analysis pipelines for HG projects
Python
1
star
49

ansible-fluent-bit

Ansible role for Fluent Bit
Shell
1
star
50

bindmapfuse

Go
1
star
51

docker-baton

baton in a Docker container
Python
1
star
52

coloc

R
1
star
53

tarbomb-disposal

Extract a tar archive, defusing any tarbombs
Shell
1
star
54

openstack-info

Gets information about what is in an OpenStack tenant
Python
1
star
55

secrets

A command line based secrets manager
Shell
1
star
56

indelible-docker

docker image instructions for Indelible
Dockerfile
1
star
57

genestack-uploader

A HTTP server providing an API and a frontend for easy uploading to Genestack
Python
1
star
58

cookie-monster

COOKIES! Om nom nom nom...
Python
1
star
59

shadowbroker

Quick tool to connect the HGI queues on RT to the MUC
Scala
1
star
60

FPGA-Evaluation

A repository of scripts and other miscellaneous things for evaluating FPGA accelerated pipelines.
Shell
1
star
61

python-rt

Clone of git://git.nic.cz/python-rt.git
Python
1
star
62

python-capturewrap

Wraps callables to capture stdout, stderr, exceptions and the return
Python
1
star
63

docker-cookhla

Dockerfile
1
star
64

github-to-gitlab-hook

Service to sync GitHub and GitLab repositories
Python
1
star
65

hgi-registry

Human Genetics Programme project and team group registry API
Python
1
star
66

hgi-cloud

terraform and ansible codebase to provision clusters (e.g. hail/spark) at Sanger
Python
1
star