Collaborative Container Modules with Singularity Registry HPC
Collaborative Container Modules with Singularity Registry HPC - Published in JOSS (2021)
Sciris
Sciris: Simplifying scientific software in Python - Published in JOSS (2023)
x11docker
x11docker: Run GUI applications in Docker containers - Published in JOSS (2019)
cwl_runner
Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊
dockstore
An app store for scientific workflows, tools, notebooks, and services
Singularity Registry
Singularity Registry: Open Source Registry for Singularity Images - Published in JOSS (2017)
Containershare
Containershare: Open Source Registry to build, test, deploy with CircleCI - Published in JOSS (2018)
cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://github.com/sylabs/singularity
SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.
udocker
A basic user tool to execute simple docker containers in batch or interactive systems without root privileges.
neurodocker
Generate custom Docker and Singularity images, and minimize existing containers
https://github.com/lablup/backend.ai
Backend.AI is a streamlined, container-based computing cluster platform that hosts popular computing/ML frameworks and diverse programming languages, with pluggable heterogeneous accelerator support including CUDA GPU, ROCm GPU, TPU, IPU and other NPUs.
jetson-containers
Machine Learning Containers for NVIDIA Jetson and JetPack-L4T
https://github.com/pachyderm/pachyderm
Data-Centric Pipelines and Data Versioning
rworkflows
Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.
scif
scientific filesystem: a filesystem organization for scientific software and metadata
https://github.com/anchore/grype
A vulnerability scanner for container images and filesystems
https://github.com/crowdstrike/falcon-scripts
Scripts to streamline the deployment and use of the CrowdStrike Falcon sensor
https://github.com/crowdstrike/falcon-operator
https://github.com/crowdstrike/container-image-scan-action
CrowdStrike Container Image Scan Github Action
https://github.com/crowdstrike/ivan
Falcon Image Vulnerability Analysis (IVAN) is a command-line image assessment tool.
https://github.com/deepfence/threatmapper
Open Source Cloud Native Application Protection Platform (CNAPP)
https://github.com/agnostiqhq/covalent-docker-dev
Dockerfiles used for building and developing Covalent in various environments
vent
Vent is a light-weight platform built to automate network collection and analysis pipelines using a flexible set of popular open source tools and technologies. Vent is python-based, extensible, leverages docker containers, and provides both an API and CLI.
singularity
command line tool for working with singularity hub and singularity containers
https://github.com/bytedance/varmor
vArmor is a cloud native container sandbox system based on AppArmor/BPF/Seccomp. It also includes multiple built-in protection rules that are ready to use out of the box.
kube-burner
Kubernetes performance and scale test orchestration framework written in golang
shpc-registry-cache
A cache of container executables (currently featuring the BioContainers) 🗃️
https://github.com/bast/apptainer-conda
Local Conda environments via Apptainer.
https://github.com/con/shub
GitHub mirror of http://datasets.datalad.org/?dir=/shub providing historical copy of containers from https://singularity-hub.org
docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
https://github.com/Trow-Registry/trow
Container Registry and Image Management for Kubernetes Clusters
https://github.com/ceems-dev/ceems
A Prometheus exporter and a REST API server to export metrics of compute units of resource managers like SLURM, Openstack, k8s, _etc_
https://github.com/databio/bulker
Manager for multi-container computing environments
https://github.com/angrymaciek/angry-runner
Docker image recipe for a self-hosted GitHub Actions runner / development environment
https://github.com/warewulf/warewulf
Warewulf is a stateless and diskless container operating system provisioning system for large clusters of bare metal and/or virtual systems.
containers-introduction-training
Course website "Docker and Singularity for reproducible research: getting started with containers"
Tesseract Core
Tesseract Core: Universal, autodiff-native software components for Simulation Intelligence - Published in JOSS (2025)
HelpMe Command Line Helper Utility
HelpMe Command Line Helper Utility - Published in JOSS (2018)
