Collaborative Container Modules with Singularity Registry HPC
Collaborative Container Modules with Singularity Registry HPC - Published in JOSS (2021)
Singularity Compose
Singularity Compose: Orchestration for Singularity Instances - Published in JOSS (2019)
Connectome Mapper 3
Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping - Published in JOSS (2022)
The Experiment Factory
The Experiment Factory: Reproducible Experiment Containers - Published in JOSS (2018)
Singularity Registry
Singularity Registry: Open Source Registry for Singularity Images - Published in JOSS (2017)
Container Tree
Container Tree: Software to Model Container Filesystems, Packages, and Inheritance - Published in JOSS (2019)
compss
COMP Superscalar (COMPSs) is a framework which aims to ease the development and execution of applications for distributed infrastructures, such as Clusters, Grids and Clouds.
plip
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
scif
scientific filesystem: a filesystem organization for scientific software and metadata
https://github.com/cokelaer/damona
singularity environment manager (application to NGS and bioinformatics)
https://github.com/aces/cbrain-containers-recipes
Recipes for singularity and docker containers used in CBRAIN
https://github.com/pc2/jhub-hpc-interface
JupyterHub + High-Performance Computing
https://github.com/alan-turing-institute/ai-workflows
A collections of portable, real-world AI workflows for testing and benchmarking
https://github.com/cokelaer/graphviz4all
dot and other graphviz executable in a simple singularity container
https://github.com/cnpem/hpc-containers
Apptainer/Singularity containers for HPC clusters
tucca-rna-seq
Tufts University Center for Cellular Agriculture's RNA-Seq Workflow for Cellular Agriculture Projects
HelpMe Command Line Helper Utility
HelpMe Command Line Helper Utility - Published in JOSS (2018)
docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
nf-gwas
A nextflow pipeline to perform state-of-the-art genome-wide association studies.
TwistMethylFlow
A NextFlow pipeline for Twist NGS DNA Methylation data analysis
parametric-nn-models
Physics-Informed Neural Network, Finite Element Method enhanced neural network, and FEM data-based neural network
https://github.com/asadprodhan/blastn
How to automatically download blastn database, run blastn, and extract blastn hit sequences?
https://github.com/asadprodhan/how-to-run-kraken2-on-hpc-using-singularity-container-and-nextflow
An intuitive tutorial on Kraken2 metagenomic analysis
https://github.com/bast/contain-r
Apptainer/Singularity container for reproducible R environments.
https://github.com/bast/apptainer-conda
Local Conda environments via Apptainer.
https://github.com/cmelab/containers
Containerized software stacks for the Computational Materials Science Lab
https://github.com/ccbr/dockers
A collection of Dockerfiles to facilitate reproducibility across computing environments.
https://github.com/coderefinery/hpc-containers
Lesson about containers for HPC with focus on 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
https://github.com/bencardoen/singularity_julia
Template definition file for Singularity RO containers with Julia and user package embedded.
mpox-seek
A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing
https://github.com/computationalproteomics/omicloupe
Understanding expression across comparisons and datasets through interactive visualization
containers-introduction-training
Course website "Docker and Singularity for reproducible research: getting started with containers"