Projects in Awesome Lists by wtsi-hgi
A curated list of projects in awesome lists by wtsi-hgi .
https://github.com/wtsi-hgi/docker-proxify
Allows building and running docker container images from behind a corporate proxy
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/yascp
scRNA multimodal analysis pipeline utilised for large dataset processing
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/openconnect-proxy
Provide an authenticated http proxy that provides connectivity via an OpenConnect VPN client (to connect to a compatible AnyConnect VPN server)
anyconnect docker http-proxy openconnect openconnect-proxy openconnect-vpn-client proxy proxy-server tunnel vpn
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/qtlight
eqtl analysis pipeline using tensorqtl, saige-qtl and LIMIX
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/gatk-cwl-generator
Generates CWL files from the GATK documentation
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/bsub_jupyter_lab
start jupyterlab python and R server on LSF farm5 node via bsub
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/rstudio_sanger_lsf_farm
bsub Rstudio server on Sanger LSF farm, with access to /lustre, to be accessed via web browser
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/consul-lock
CLI and Python interface for easily managing Consul locks
cli consul distributed-locks library python tool
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/ansible-style-guide
Style guide for writing Ansible
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/python-hgijson
Python library for easily JSON encoding/decoding complex class-based Python models, using an arbitrarily complex (but easy to write!) mapping schema.
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/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.
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/nf_scrna_qc
Single cell RNA-seq quality control, transcription profile clustering & cell-type assignment
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/gitlab-build-variables
Tools for managing GitLab CI pipeline build variables
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/mpistat
Efficiently lstat every file in a filesystem tree in parallel across multiple nodes using MPI.
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/arvados-pipelines
HGI arvados pipelines (crunch scripts, container Dockerfiles, pipeline templates, etc)
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/hgi-systems
Orchestration and configuration management of hgi systems (using terraform & ansible)
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/metadata-check
Tests to perform on the iRODS metadata for a BAM file, versus the information in the file header
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/13amp
Userspace CRAM-to-BAM translation virtual filesystem
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/yatadis
Yet Another Terraform Ansible Dynamic Inventory Script (yatadis)
ansible ansible-inventory terraform
Last synced: 14 Mar 2025
https://github.com/wtsi-hgi/nf_cellbender
Single cell Nextflow cellbender pipeline.
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/hapi-ur
HAPI-UR: HAPlotype Inference for UnRelated samples (cloned from: https://code.google.com/p/hapi-ur)
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/wes-qc
Sample and variant QC for exome cohort studies
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/ldapvi
Clone of ldapvi from http://www.lichteblau.com/git/ldapvi.git
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/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
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/lustre_operator
Wrapper script to allow non-root users to run privileged lfs commands on particular Lustre filesystems (using sudo)
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/cwl-graph-generate
Generates https://view.commonwl.org/ like workflows images, showing a complete workflow.
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/vareval
A collection of scripts for evaluating variant callers
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/bindmapfuse
bind-mount docker filesystem fuse passthrough
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/www-hierarchical-fairshare
Tools to view LSF hierarchical fairshare UserGroup shares and current priority (e.g. in a treemap)
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/python-capturewrap
Wraps callables to capture stdout, stderr, exceptions and the return
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/secrets
A command line based secrets manager
bash blockchain gnupg gpg password-manager
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/fpga-evaluation
A repository of scripts and other miscellaneous things for evaluating FPGA accelerated pipelines.
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/hail_analysis_pipelines
Hail based analysis pipelines for HG projects
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/single_cell
Single Cell pipelines used at Sanger
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/docker-eigensoft
Dockerised EIGENSOFT software (https://github.com/DReichLab/EIG)
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/github-to-gitlab-hook
Service to sync GitHub and GitLab repositories
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/seq_autoqc
Additional high-throughput sequencing autoQC steps
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/irodsa-utilities
Convenience scripts for reading/creating the contents of .irodsA files
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/olly-maersk
Containerisation-agnostic LSF execution configuration for Cromwell
cromwell docker lsf singularity
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/python-rt
Clone of git://git.nic.cz/python-rt.git
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/nf_scrna_deconvolution
CellSNP-Vireo deconvolution pipeline, with optional genotype input.
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/helpful-genestack-scripts
Some useful scripts for use with genestack
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/exomeqc-hail-gnomad
Code repository for sample and variant qc for Sanger cohorts using hail and gnomad qc code.
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/shadowbroker
Quick tool to connect the HGI queues on RT to the MUC
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/indelible-docker
docker image instructions for Indelible
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/yggdrasil
Node.js framework for hypr-based graph information systems
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/genestack-uploader
A HTTP server providing an API and a frontend for easy uploading to Genestack
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/openstack-info
Gets information about what is in an OpenStack tenant
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/ebi-ngs-workshop
HGI's materials for the EBI Next Generation Sequencing (NGS) workshop
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/tarbomb-disposal
Extract a tar archive, defusing any tarbombs
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/hgc-tools
Set of tools for working with Mercury capsules.
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/docker-arvados-dev
Docker container for Arvados development (and running tests)
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/cluster-launcher
A tool to bring up clusters launched via osdataproc. Repo found: https://github.com/wtsi-ssg/osdataproc
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/bdist
Submit a distributed job to your LSF compute cluster
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/nf_splicing
a pipeline for splicing analysis using short reads
Last synced: 17 Feb 2025
https://github.com/wtsi-hgi/condapaths
Extract conda-related paths from wrstat stats.gz files
Last synced: 13 Mar 2025
https://github.com/wtsi-hgi/unjsify_cwl
Converts CWL Inline Javascript expressions into explicit processing steps
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/hgi-web_usermod
User roles authentication module for HGI-web
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/imirror
Copy a directory to iRODS and distribute the work over an LSF cluster
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/irobot-client
Basic client to interact with the iRobot HTTP API
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/ansible-supergiant
Ansible role for configuring Supergiant
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/ibackup
Performant backups of many files to iRODS
Last synced: 15 Apr 2025
https://github.com/wtsi-hgi/thrifty-builder
Builds Docker images, capturing information to reduce the frequency of future re-builds
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/python-common
[DEPRECATED] Python 3 common library
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/sync-ldap-lustre-irods
Tool to synchronise iRods and POSIX Users
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/openstack-tools
Tools for working with OpenStack
Last synced: 22 Mar 2025
https://github.com/wtsi-hgi/openstack_report
A web application to generate usage report for hail clusters
Last synced: 22 Mar 2025