GitHub topics: singularity
netreconlab/ca-server
A Certificate Authority (CA) Server written in python using fastAPI
Language: ASP.NET - Size: 460 KB - Last synced at: about 6 hours ago - Pushed at: about 7 hours ago - Stars: 11 - Forks: 1
seqeralabs/wave
On-demand containers provisioning service
Language: Groovy - Size: 31.6 MB - Last synced at: about 15 hours ago - Pushed at: about 16 hours ago - Stars: 37 - Forks: 5
apptainer/singularity
Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.
Language: Go - Size: 34.8 MB - Last synced at: about 16 hours ago - Pushed at: over 2 years ago - Stars: 2,563 - Forks: 427
sliming-ai/sliming-ai.github.io
🧠 Singular values-driven automated filter pruning
Language: JavaScript - Size: 384 MB - Last synced at: about 22 hours ago - Pushed at: about 23 hours ago - Stars: 7 - Forks: 3
singularityhub/shpc-registry
A remote registry for Singularity Registry HPC 🖊️
Language: Shell - Size: 3.12 GB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 13 - Forks: 18
nextflow-io/nextflow
A DSL for data-driven computational pipelines
Language: Groovy - Size: 58 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 2,909 - Forks: 680
opensciencegrid/cvmfs-singularity-sync
Scripts to synchronize Singularity images to a CVMFS repository.
Language: Python - Size: 745 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 24 - Forks: 150
apptainer/apptainer
Apptainer: Application containers for Linux
Language: Go - Size: 39.8 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 1,282 - Forks: 148
StaPH-B/docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
Language: Dockerfile - Size: 107 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 206 - Forks: 129
mkkoshkina/wf_denovo_sequencing
This is a Snakemake pipeline for de novo sequencing and annotation of MS peptidomics data
Language: Python - Size: 24.4 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0
biocorecrg/master_of_pores
Nextflow pipeline for analysis of direct RNA Nanopore reads
Language: Nextflow - Size: 448 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 101 - Forks: 17
dz333n/Singularity-OS
Microsoft Research Singularity RDK 2.0 Source
Language: C# - Size: 82.1 MB - Last synced at: 3 days ago - Pushed at: almost 5 years ago - Stars: 62 - Forks: 11
ENCCS/upscalingAIworkflows
Lesson material for Upscaling AI workflows
Language: Jupyter Notebook - Size: 11.2 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 2
ENCCS/containers 📦
Containers Lessons
Language: Python - Size: 3 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 1
tucca-cellag/tucca-rna-seq
[UNDER-CONSTRUCTION] TUCCA's RNA-Seq Snakemake Workflow for Cellular Agriculture Projects
Language: Python - Size: 845 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1 - Forks: 0
CDCgov/tostadas
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
Language: Python - Size: 49.6 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 27 - Forks: 13
singularityhub/singularity-catalog
The Singularity Community Catalog of Singularity* recipe files.
Language: Singularity - Size: 205 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 11 - Forks: 2
glotzerlab/hoomd-blue
Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
Language: C++ - Size: 71.3 MB - Last synced at: 8 days ago - Pushed at: 10 days ago - Stars: 368 - Forks: 139
tomeichlersmith/denv
uniformly interact with containerized environments across runners
Language: Shell - Size: 457 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 7 - Forks: 1
seqeralabs/wave-cli
Command line tool for Wave containers provisioning service
Language: Java - Size: 410 KB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 14 - Forks: 3
singularityhub/singularity-hpc
Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.
Language: Python - Size: 11.9 MB - Last synced at: 7 days ago - Pushed at: 10 days ago - Stars: 118 - Forks: 27
pharmai/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
Language: Python - Size: 8.98 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 519 - Forks: 113
ImagoXV/NanoASV
NanoASV official repo
Language: Shell - Size: 86.4 MB - Last synced at: 10 days ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 3
mbhall88/container_recipes
Repository with all my container recipes 👩🍳
Language: Dockerfile - Size: 99.6 KB - Last synced at: 4 days ago - Pushed at: 7 months ago - Stars: 16 - Forks: 6
unlhcc/singularity-dockerfiles
Read-only mirror of the HCC singularity dockerfiles repo.
Language: C++ - Size: 30.1 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 7 - Forks: 6
CCBR/Dockers
A collection of Dockerfiles to facilitate reproducibility across computing environments.
Language: Dockerfile - Size: 934 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 11 - Forks: 3
JD2112/TwistMethNext
A NextFlow pipeline for Twist NGS DNA Methylation data analysis
Language: HTML - Size: 28.2 MB - Last synced at: 9 days ago - Pushed at: 14 days ago - Stars: 1 - Forks: 0
NVIDIA/hpc-container-maker
HPC Container Maker
Language: Python - Size: 2.06 MB - Last synced at: 9 days ago - Pushed at: 26 days ago - Stars: 475 - Forks: 96
pscedu/singularity-octave
GNU Octave is software featuring a high-level programming language, primarily intended for numerical computations
Language: Shell - Size: 125 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 0 - Forks: 1
connectomicslab/connectomemapper3
Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.
Language: HTML - Size: 354 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 73 - Forks: 29
FoamScience/openfoam-apptainer-packaging
Ansible playbooks for automated builds of Apptainer containers of HPC packages; focusing on OpenFOAM
Language: C++ - Size: 70.3 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 8 - Forks: 0
bsc-wdc/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.
Language: Java - Size: 288 MB - Last synced at: 9 days ago - Pushed at: 18 days ago - Stars: 51 - Forks: 21
netreconlab/parse-hipaa
HIPAA & GDPR compliant ready parse-server with postgres/mongo, parse-hipaa-dashboard. Compatible with ParseCareKit
Language: JavaScript - Size: 13.8 MB - Last synced at: 17 days ago - Pushed at: 18 days ago - Stars: 103 - Forks: 44
autistic-symposium/singularity.sh-blog-generator 📦
👾 old blog on security, hacking, and machine learning
Language: HTML - Size: 307 MB - Last synced at: about 1 hour ago - Pushed at: 6 months ago - Stars: 5 - Forks: 0
jcaperella29/ATAC_APP
Interactive Shiny app for annotating MACS2 ATAC-seq peaks and visualizing functional enrichment (GO, KEGG, Reactome) — fully containerized for Docker & HPC.
Language: R - Size: 48.8 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0
expfactory/expfactory
software to generate a reproducible container with a battery of experiments
Language: Python - Size: 2.53 MB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 38 - Forks: 14
vsoch/scif
scientific filesystem: a filesystem organization for scientific software and metadata
Language: Python - Size: 569 KB - Last synced at: 10 days ago - Pushed at: about 1 year ago - Stars: 34 - Forks: 12
singularityhub/docker2singularity
A docker image for converting docker images to singularity images.
Language: Shell - Size: 302 KB - Last synced at: 16 days ago - Pushed at: 9 months ago - Stars: 288 - Forks: 34
sib-swiss/containers-introduction-training
Course website "Docker and Singularity for reproducible research: getting started with containers"
Language: HTML - Size: 22.9 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 31 - Forks: 14
OpenOmics/mir-seek
An awesome microRNA-sequencing pipeline
Language: Python - Size: 595 KB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 1
afbjorklund/unsingularity
Extract files from SIF file
Language: Shell - Size: 9.77 KB - Last synced at: 5 days ago - Pushed at: 22 days ago - Stars: 1 - Forks: 0
pscedu/singularity
Just a list of Singularity definition files maintained by the Biomed Applications Group
Language: Python - Size: 182 KB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 0 - Forks: 0
pscedu/singularity-stride
Protein secondary structure assignment
Language: Shell - Size: 8.79 KB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 0 - Forks: 0
vmikk/PhyloNext
A pipeline for phylogenetic diversity analysis of GBIF-mediated data
Language: R - Size: 18.1 MB - Last synced at: 19 days ago - Pushed at: 3 months ago - Stars: 13 - Forks: 1
OpenOmics/nanite
A streamlined Oxford Nanopore Viral Metagenomics Pipeline
Language: Python - Size: 627 KB - Last synced at: 9 days ago - Pushed at: 25 days ago - Stars: 4 - Forks: 2
genepi/nf-gwas
A nextflow pipeline to perform state-of-the-art genome-wide association studies.
Language: Nextflow - Size: 65.2 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 65 - Forks: 26
getpopper/popper
Container-native task automation engine.
Language: Python - Size: 1.43 MB - Last synced at: 4 days ago - Pushed at: about 3 years ago - Stars: 303 - Forks: 61
ZuberLab/crispr-mageck-nf
Analyze CRISPR and shRNA functional genetic screening data
Language: R - Size: 59.6 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 9 - Forks: 5
netreconlab/hipaa-postgres
HIPAA & GDPR compliant ready Postgres Database with PostGIS and PGAuditor
Language: Shell - Size: 185 KB - Last synced at: 28 days ago - Pushed at: 29 days ago - Stars: 12 - Forks: 2
ejLw/registry-template
A template for running your own registry.
Size: 1000 Bytes - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 0 - Forks: 0
JuliaContainerization/SimpleContainerGenerator.jl
Create container images for using Julia packages (especially useful in environments without Internet access)
Language: Julia - Size: 139 KB - Last synced at: 12 days ago - Pushed at: over 3 years ago - Stars: 94 - Forks: 3
kaczmarj/apptainer-in-docker
Apptainer in Docker!
Language: Dockerfile - Size: 24.4 KB - Last synced at: 1 day ago - Pushed at: 5 months ago - Stars: 46 - Forks: 10
alan-turing-institute/AI-workflows 📦
A collections of portable, real-world AI workflows for testing and benchmarking
Language: Shell - Size: 263 KB - Last synced at: 13 days ago - Pushed at: almost 3 years ago - Stars: 8 - Forks: 1
netreconlab/parse-hipaa-dashboard
Parse Dashboard for parse-hipaa server
Language: JavaScript - Size: 2.02 MB - Last synced at: 23 days ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 0
OpenOmics/mpox-seek
A rapid pipeline for targeted ONT monkeypox sequencing
Language: Python - Size: 593 KB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0
OpenOmics/modr
An awesome Oxford Nanopore Pipeline for direct RNA-sequencing
Language: Python - Size: 689 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 1
OpenOmics/metavirs
Viral Metagenomics Assembly and Annotation Pipeline
Language: Python - Size: 695 KB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 1
OpenOmics/cyte-seek
Awesome single-cell CITE-sequencing Pipeline
Language: Python - Size: 708 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0
OpenOmics/HiIP
An awesome Hi-C + ChIP (HiChIP) sequencing pipeline.
Language: Python - Size: 577 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
OpenOmics/ervx
Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with bulk RNA
Language: Python - Size: 908 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 1
skchronicles/RNA-seek
A comprehensive quality-control and quantification RNA-seq pipeline
Language: Python - Size: 10.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 13
singularityhub/singularity2docker
convert a singularity image back to Docker, full circle! #containerfriends
Language: Shell - Size: 28.3 KB - Last synced at: 11 days ago - Pushed at: almost 5 years ago - Stars: 24 - Forks: 9
PangzeCheung/SingDiffusion
[CVPR 2024] Tackling the Singularities at the Endpoints of Time Intervals in Diffusion Models
Language: Python - Size: 23.4 KB - Last synced at: 25 days ago - Pushed at: about 1 year ago - Stars: 66 - Forks: 4
Rick-van-Dam/Singularity 📦
A extremely fast ioc container for high performance applications
Language: C# - Size: 16.3 MB - Last synced at: 5 days ago - Pushed at: over 4 years ago - Stars: 77 - Forks: 12
Five-Research/five-research.github.io
checkout our awesome website here
Language: HTML - Size: 7.02 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
cokelaer/damona
singularity environment manager (application to NGS and bioinformatics)
Language: Python - Size: 6.91 MB - Last synced at: 7 days ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 2
asadprodhan/blastn
How to automatically download blastn database, run blastn, and extract blastn hit sequences?
Language: Shell - Size: 303 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0
pc2/JHub-HPC-Interface
JupyterHub + High-Performance Computing
Language: Jupyter Notebook - Size: 449 KB - Last synced at: 8 days ago - Pushed at: almost 4 years ago - Stars: 6 - Forks: 1
singularityhub/install-singularity
Action to install Singlarity optimized for simplicity.
Size: 72.3 KB - Last synced at: 11 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 2
ucla-oarc-hpc/hpc_containers
Collection of Dockerfiles and Apptainer files used to create containers on Hoffman2
Language: Roff - Size: 92.8 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
GaneshShivalingappa/Parametric-NN-Models
Physics-Informed Neural Network, Finite Element Method enhanced neural network, and FEM data-based neural network
Language: Python - Size: 177 KB - Last synced at: 10 days ago - Pushed at: about 2 months ago - Stars: 18 - Forks: 0
UPHL-BioNGS/Grandeur
UPHL's Reference Free Pipeline
Language: Nextflow - Size: 512 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 26 - Forks: 7
singularityhub/github-ci
An example GitHub Action (CI) to build a Singularity container
Language: Singularity - Size: 69.3 KB - Last synced at: 7 days ago - Pushed at: almost 2 years ago - Stars: 69 - Forks: 28
pydicom/dicom-containers
singularity and Docker containers to easily get started with common dicom tools
Language: Dockerfile - Size: 31.3 KB - Last synced at: 15 days ago - Pushed at: almost 5 years ago - Stars: 22 - Forks: 1
singularityhub/singularity-compose
orchestration for singularity containers (under development)
Language: Python - Size: 6.67 MB - Last synced at: 7 days ago - Pushed at: 12 months ago - Stars: 74 - Forks: 17
mattgalbraith/singularity-docker
Build Docker container for Apptainer/Singularity software
Language: Dockerfile - Size: 3.91 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
jaantollander/julia-apptainer
Example of installing Julia package inside an Apptainer container and running it from the container.
Language: Julia - Size: 2.93 KB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
remotesensinginfo/docker_builds
A set of docker build scripts used to build the docker images (which I import into singularity) for my processing chains.
Language: Dockerfile - Size: 41 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 2
bdusell/singularity-tutorial
Tutorial for using Singularity containers
Size: 6.33 MB - Last synced at: 12 days ago - Pushed at: over 4 years ago - Stars: 116 - Forks: 11
dgruber/wfl
A Simple Way of Creating Job Workflows in Go running in Processes, Containers, Tasks, Pods, or Jobs
Language: Go - Size: 179 MB - Last synced at: 15 days ago - Pushed at: 4 months ago - Stars: 47 - Forks: 8
nextflow-io/nf-hack17-tutorial 📦
Nextflow basic tutorial for newbie users
Language: Nextflow - Size: 438 KB - Last synced at: about 2 months ago - Pushed at: almost 7 years ago - Stars: 33 - Forks: 18
singularityhub/singularity-cli
streamlined singularity python client (spython) for singularity
Language: Python - Size: 8.86 MB - Last synced at: 13 days ago - Pushed at: 7 months ago - Stars: 59 - Forks: 31
singularityhub/stools
singularity container tools for continuous integration and quality assessment
Language: Python - Size: 174 KB - Last synced at: 11 days ago - Pushed at: almost 2 years ago - Stars: 10 - Forks: 2
pmitev/Teoroo-singularity
Singularity images and recipes
Language: JavaScript - Size: 5.38 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
ZuberLab/crispr-process-nf
Process CRISPR and shRNA functional genetic screening data
Language: Nextflow - Size: 1.59 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 1
pmitev/UPPMAX-Singularity-workshop
Online material for the UPPMAX Singularity workshop
Language: Shell - Size: 2.86 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 7 - Forks: 2
DMackRus/Apptainer_GPU_Physics_Simulators
An Apptainer/Singularity container for using various GPU-based physics simulators (mujoco-mjx, genesis)
Language: Shell - Size: 14.6 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
jacksonwalters/elliptic-curves-finite-fields
Examining the curve y^2=x^3+x+1 over various fields, including \QQ, \CC, F_2, and F_7.
Language: Jupyter Notebook - Size: 6.67 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1
ucla-oarc-hpc/WS_containers
Hoffman2 Workshop on Containers
Language: Python - Size: 37.3 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
spm/spm-docker
SPM Containers (Docker & Singularity)
Language: Dockerfile - Size: 101 KB - Last synced at: 6 days ago - Pushed at: 5 months ago - Stars: 21 - Forks: 12
juliawiggeshoff/singularity-recipes
Recipes for Singularity
Size: 31.3 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
MPUSP/snakemake-bacterial-riboseq
Bacterial-Riboseq: A Snakemake workflow for the analysis of riboseq data in bacteria.
Language: Python - Size: 943 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0
vmikk/biodiverse-docker
Docker and Singularity images to run Biodiverse software
Language: Perl - Size: 35.2 KB - Last synced at: 16 days ago - Pushed at: 3 months ago - Stars: 0 - Forks: 1
netreconlab/pmm-server
This repo provides a Singularity image version for Percona Monitoring and Management (PMM)
Language: Singularity - Size: 32.2 KB - Last synced at: 22 days ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
netreconlab/hipaa-mongo
HIPAA & GDPR compliant ready Mongo Database with percona-server.
Language: Dockerfile - Size: 81.1 KB - Last synced at: 23 days ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 1
ankushgpta2/tostadas Fork of CDCgov/tostadas
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
Language: Python - Size: 1.36 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
MPUSP/snakemake-ont-bacterial-variants
A Snakemake workflow for the identification of variants in bacterial genomes using nanopore long-read sequencing.
Language: Python - Size: 28.8 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0
Flamisell/StewartPlatformLocalSingularityAvoidance_py
Stweart Platform Simulation with Trapezoidal Velocity Trajectory Planner and Local Singularity Avoidance
Language: Jupyter Notebook - Size: 1.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
singularityhub/sregistry-cli
Singularity Global Client for container management
Language: Python - Size: 2.64 MB - Last synced at: 11 days ago - Pushed at: almost 2 years ago - Stars: 15 - Forks: 17
pscedu/singularity-guppy
Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms.
Language: Shell - Size: 14.6 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0