wtsi-hgi/r-spack-recipe-builder

Spack recipe creator for R packages in CRAN and Bioconductor used to build up the ubeR module for use in farm22

Language: Python - Size: 305 KB - Last synced: about 3 hours ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

wtsi-hgi/go-farmer

Language: Go - Size: 11.7 KB - Last synced: about 4 hours ago - Pushed: about 5 hours ago - Stars: 0 - Forks: 0

wtsi-hgi/admixture-from-glimpse

Run admixture on GLIMPSE imputed genotypes to predict sample populations

Language: Nextflow - Size: 26.4 KB - Last synced: about 5 hours ago - Pushed: about 22 hours ago - Stars: 0 - Forks: 0

wtsi-hgi/spack-repo

Spack Package Repository

Language: Python - Size: 26.8 MB - Last synced: about 19 hours ago - Pushed: about 22 hours ago - Stars: 1 - Forks: 3

wtsi-hgi/wes-qc

Sample and variant QC for exome cohort studies

Language: Jupyter Notebook - Size: 13.5 MB - Last synced: about 23 hours ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

wtsi-hgi/mercuryrc

Language: Shell - Size: 104 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 0

wtsi-hgi/farmers-report

Weekly report for farm usage

Language: R - Size: 74.2 KB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0

wtsi-hgi/softpack-web

Softpack Web provides a graphical user interface for Softpack services.

Language: TypeScript - Size: 1.73 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

wtsi-hgi/glimpse-nextflow

Language: Nextflow - Size: 35.2 KB - Last synced: 20 days ago - Pushed: 22 days ago - Stars: 0 - Forks: 0

wtsi-hgi/wtsi-hgi.github.io

Github webpage for HGI projects

Language: HTML - Size: 21.5 KB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 0 - Forks: 0

wtsi-hgi/sarek

Language: Nextflow - Size: 33.3 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 0 - Forks: 1

wtsi-hgi/MAVEQC

Language: R - Size: 511 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

wtsi-hgi/softpack-builder

SoftPack Builder provides services for building SoftPack environments

Language: Python - Size: 1.61 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

wtsi-hgi/nf_tower_irods_to_lustre

Language: Nextflow - Size: 111 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 1

wtsi-hgi/yascp

scRNA analysis pipeline

Language: Python - Size: 119 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 9 - Forks: 6

wtsi-hgi/go-softpack-builder

Go implementation of a softpack builder service

Language: Go - Size: 198 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

wtsi-hgi/coloc-flow

Language: Nextflow - Size: 2.58 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 1

wtsi-hgi/nf_scrna_qc

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

Language: Python - Size: 194 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 2

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)

Language: Shell - Size: 1.95 KB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 12 - Forks: 6

wtsi-hgi/QTLight

Language: Python - Size: 10.6 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 6 - Forks: 4

wtsi-hgi/SSDV

Language: JavaScript - Size: 20.1 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 2 - Forks: 3

wtsi-hgi/spack-repo-testing Fork of wtsi-hgi/spack-repo

Spack Package Repository (static version for tests)

Size: 658 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

wtsi-hgi/conda-audited

Wrapper script to and audit and configure miniconda and micromamba

Size: 19.5 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

wtsi-hgi/nf_irods_to_lustre

Fetch Cram files and/or Cellranger data from Sanger Irods to /lustre

Language: Python - Size: 104 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 3

wtsi-hgi/sync-versions-poetry

Keep pre-commit additional_dependencies in sync with dependencies pinned by Poetry.

Language: Go - Size: 67.4 KB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

wtsi-hgi/docker-proxify

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

Language: Perl - Size: 23.4 KB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 83 - Forks: 16

wtsi-hgi/hgi-systems

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

Language: HCL - Size: 3.07 MB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 4 - Forks: 3

wtsi-hgi/rstudio_sanger_lsf_farm

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

Language: Shell - Size: 75.2 KB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 4 - Forks: 1

wtsi-hgi/bsub_jupyter_lab

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

Language: Python - Size: 124 KB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 6 - Forks: 5

wtsi-hgi/exomeQC-hail-gnomad

Code repository for sample and variant qc for Sanger cohorts using hail and gnomad qc code.

Language: Jupyter Notebook - Size: 59.7 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 2

wtsi-hgi/go-softpack-analytics

Language: Go - Size: 6.84 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

wtsi-hgi/nf_cellbender

Single cell Nextflow cellbender pipeline.

Language: Python - Size: 177 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

wtsi-hgi/softpack-env-from-module

Create an environment from an SHPC-style module file.

Language: Shell - Size: 4.88 KB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

wtsi-hgi/olly-maersk

Containerisation-agnostic LSF execution configuration for Cromwell

Language: Shell - Size: 72.3 KB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0

wtsi-hgi/softpack-templates

Spack Templates

Language: Python - Size: 12.7 KB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

wtsi-hgi/sgeQC

MAVE/SGE QC R package

Language: HTML - Size: 57.6 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

wtsi-hgi/rna_seq Fork of wtsi-hgi/nextflow_ci

Language: Nextflow - Size: 181 KB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

wtsi-hgi/softpack-core

SoftPack Core

Language: Python - Size: 1.75 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

wtsi-hgi/cwl-graph-generate

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

Language: Python - Size: 6.84 KB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 2 - Forks: 2

wtsi-hgi/aeg-scrambler

AEG SCRAMBLEr

Language: Python - Size: 245 KB - Last synced: about 2 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

wtsi-hgi/docker-eigensoft

Dockerised EIGENSOFT software (https://github.com/DReichLab/EIG)

Size: 17.6 KB - Last synced: about 2 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 1

wtsi-hgi/godirwalk Fork of karrick/godirwalk

Fast directory traversal for Golang

Language: Go - Size: 242 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

wtsi-hgi/dockerfile_definitions

Here we store the Definition files for Dockerfiles and singularity files

Language: Dockerfile - Size: 3.91 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

wtsi-hgi/Automated-Enhancer-Gene-SCRAMBLEr

A tool to help automate the Genome Scramble project

Size: 867 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1

wtsi-hgi/supergiant Fork of tchen0123/supergiant

Automatically scale hardware and easily run stateful applications using Kubernetes.

Language: Go - Size: 7.97 MB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

wtsi-hgi/softpack-iac

SoftPack Infrastructure as Code

Language: HCL - Size: 81.1 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

wtsi-hgi/softpack-docs

SoftPack Documentation

Language: JavaScript - Size: 3.37 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

wtsi-hgi/openstack-info

Gets information about what is in an OpenStack tenant

Language: Python - Size: 61.5 KB - Last synced: 28 days ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

wtsi-hgi/bd-rhapsody

Language: Common Workflow Language - Size: 138 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

wtsi-hgi/grand Fork of ernsheong/grand

Grand is a Go random string generator

Language: Go - Size: 9.77 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

wtsi-hgi/cwltool Fork of common-workflow-language/cwltool 📦

Common Workflow Language reference implementation

Language: Web Ontology Language - Size: 7.15 MB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

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.

Language: JavaScript - Size: 180 KB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 5 - Forks: 8

wtsi-hgi/useintest 📦

I don't care how it's done, I just want to use it in my tests!

Language: Python - Size: 502 KB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

wtsi-hgi/docker-cookhla

Language: Dockerfile - Size: 1000 Bytes - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

wtsi-hgi/bam2cram-check

Language: Python - Size: 379 KB - Last synced: about 2 months ago - Pushed: over 7 years ago - Stars: 3 - Forks: 2

wtsi-hgi/nodervisor Fork of Stii/nodervisor

Supervisor manager in node.js

Language: JavaScript - Size: 1.07 MB - Last synced: about 2 months ago - Pushed: about 8 years ago - Stars: 3 - Forks: 2

wtsi-hgi/robot_day

Language: Python - Size: 20.5 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

wtsi-hgi/gitlab-build-variables

Tools for managing GitLab CI pipeline build variables

Language: Python - Size: 70.3 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 3 - Forks: 1

wtsi-hgi/FPGA-Evaluation

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

Language: Shell - Size: 27.3 KB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

wtsi-hgi/nf_scrna_deconvolution

CellSNP-Vireo deconvolution pipeline, with optional genotype input.

Language: Nextflow - Size: 182 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 1

wtsi-hgi/go-authserver

A library to easily create an authenticated web server in Go

Language: Go - Size: 94.7 KB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

wtsi-hgi/nf_deepvariant

Language: Nextflow - Size: 131 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 3

wtsi-hgi/ibackup

Performant backups of many files to iRODS

Language: Go - Size: 588 KB - Last synced: 1 day ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

wtsi-hgi/13amp

Userspace CRAM-to-BAM translation virtual filesystem

Language: C - Size: 402 KB - Last synced: about 2 months ago - Pushed: over 8 years ago - Stars: 2 - Forks: 1

wtsi-hgi/ansible-style-guide

Style guide for writing Ansible

Size: 19.5 KB - Last synced: about 2 months ago - Pushed: almost 6 years ago - Stars: 4 - Forks: 3

wtsi-hgi/genestack-uploader

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

Language: Python - Size: 455 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

wtsi-hgi/single_cell_annotation

Language: Python - Size: 155 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 3 - Forks: 1

wtsi-hgi/nfTower_generator Fork of edgano/nfTower_generator

Language: Shell - Size: 36.1 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

wtsi-hgi/lustre-usage-db-transfer

For transferring lustre usage data from the old schema to the new one.

Language: Go - Size: 22.5 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/hgi-vault-dev

Language: Shell - Size: 52.7 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/HUVEC

Size: 47.1 MB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/hgi-vault

Data retention policy tools

Language: Python - Size: 562 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

wtsi-hgi/tar-mtime-zero

Language: Python - Size: 137 KB - Last synced: about 2 months ago - Pushed: almost 9 years ago - Stars: 0 - Forks: 0

wtsi-hgi/tabula Fork of nc6/tabula

Project logging and analysis in the console.

Language: Haskell - Size: 122 KB - Last synced: about 2 months ago - Pushed: about 8 years ago - Stars: 6 - Forks: 0

wtsi-hgi/mpistat

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

Language: Python - Size: 70.3 KB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 3 - Forks: 4

wtsi-hgi/metadata-check

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

Language: Python - Size: 47.8 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 3

wtsi-hgi/vault-shift-mtimes

Language: Python - Size: 4.88 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/indelible-docker

docker image instructions for Indelible

Language: Dockerfile - Size: 36.1 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

wtsi-hgi/associations

This repository is for assotiations testing.

Language: Nextflow - Size: 2.05 MB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/beaver

HGI's Software Provisioning Solution

Language: Python - Size: 153 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/osdataproc Fork of wtsi-ssg/osdataproc

osdataproc is a command-line tool for creating an OpenStack cluster with Apache Spark and Apache Hadoop configured. It comes with JupyterLab and Hail, a genomic data analysis library built on Spark installed, as well as Netdata for monitoring.

Language: Jinja - Size: 266 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 2

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

Language: Vue - Size: 3 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

wtsi-hgi/crook

Language: Python - Size: 85.9 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/hail_analysis_pipelines

Hail based analysis pipelines for HG projects

Language: Python - Size: 565 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 2

wtsi-hgi/nextflow-pipelines

Nextflow HGI pipelines

Language: Nextflow - Size: 88.4 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 4 - Forks: 2

wtsi-hgi/scrna_deconvolution_container

Language: Dockerfile - Size: 74.2 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/lurge

Processes information about Lustre usage

Language: Python - Size: 628 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

wtsi-hgi/nf_tensorqtl

single-cell eQTL mapping using tensorQTL (linear models)

Language: Python - Size: 71.3 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/scrna_cellbender_container

Language: Dockerfile - Size: 57.6 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/hail_jc_merge

hail scripts for merging cohorts

Language: Jupyter Notebook - Size: 106 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/vault-prerun-reporter

A tool to give reports on what Vault will delete when we launch it on a project directory

Language: Python - Size: 22.5 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/helpful-genestack-scripts

Some useful scripts for use with genestack

Language: Shell - Size: 61.5 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

wtsi-hgi/svscore_container

Language: Dockerfile - Size: 6.84 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/docker-icat

iRODS server in a Docker container

Language: Shell - Size: 49.8 KB - Last synced: about 2 months ago - Pushed: over 7 years ago - Stars: 1 - Forks: 1

wtsi-hgi/consul-lock

CLI and Python interface for easily managing Consul locks

Language: Python - Size: 167 KB - Last synced: 25 days ago - Pushed: over 2 years ago - Stars: 4 - Forks: 1

wtsi-hgi/weaver

Browser-based Shiny frontend to view internal Lustre volume reports

Language: R - Size: 408 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/docker-hla-tapas

Dockerised HPA-TAPAS

Language: Dockerfile - Size: 1.95 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

wtsi-hgi/genestack-study-viewer

Easily view metadata from studies from genestack

Language: R - Size: 58.6 KB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

wtsi-hgi/crispr_container

Language: Dockerfile - Size: 61.5 KB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

wtsi-hgi/single_cell

Single Cell pipelines used at Sanger

Language: Shell - Size: 24.4 KB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0