singularity

There are 5 repositories under singularity topic.

nextflow
nextflow-io / nextflow
A DSL for data-driven computational pipelines
bioinformatics workflow-engine pipeline pipeline-framework nextflow cloud groovy sge slurm aws docker singularity hpc singularity-containers reproducible-science reproducible-research dataflow hello
Language:Groovy 2664
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.
cloud-native container containers hpc linux parallel portability portable reproducible reproducible-science rootless-containers science singularity singularity-container
Language:Go 2519
apptainer / apptainer
Apptainer: Application containers for Linux
apptainer containers hpc linux rootless-containers science singularity singularity-container
Language:Go 1034
NVIDIA / hpc-container-maker
HPC Container Maker
containers docker hpc singularity
Language:Python 445
plip
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
scientific-computing bioinformatics protein-structure plip singularity python-bindings openbabel pdb docker
Language:Python 440
glotzerlab / hoomd-blue
Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
cuda python molecular-dynamics hard-particle hoomd-blue simulation gpu singularity docker conda-forge particle-system monte-carlo-simulation
Language:C++ 329
getpopper / popper
Container-native task automation engine.
reproducibility cli devops sciops containers workflows docker singularity podman automation-engine
Language:Python 301
singularityhub / docker2singularity
A docker image for converting docker images to singularity images.
docker docker-image singularity singularity-images
Language:Shell 277
Azure / batch-shipyard
Simplify HPC and Batch workloads on Azure
azure-batch docker hpc mpi gpu infiniband rdma azure batch-processing nfs glusterfs azure-functions containers singularity windows-containers serverless slurm
Language:Python 276
StaPH-B / docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
bioinformatics containers docker dockerfiles singularity
Language:Dockerfile 181
Sarek
SciLifeLab / Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
nextflow workflow pipeline bioinformatics genomics cancer next-generation-sequencing docker singularity reproducible-science reproducible-research containers germline germline-variants somatic somatic-variants
Language:Nextflow 132
x11vnc / x11vnc-desktop
Docker/Singularity image for Ubuntu with X11 and VNC
docker ubuntu x11 vnc websocket novnc html5 singularity
Language:Python 119
sylabs / wlm-operator
Singularity implementation of k8s operator for interacting with SLURM.
kubernetes k8s slurm kubernetes-operator singularity hpc
Language:Go 117
sylabs / singularity-cri
The Singularity implementation of the Kubernetes Container Runtime Interface
singularity-cri cri singularity kubernetes hpc containers
Language:Go 114
bdusell / singularity-tutorial
Tutorial for using Singularity containers
singularity container cuda pytorch cudnn
112
singularity-hpc
singularityhub / singularity-hpc
Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.
containers hpc lmod reproducibility singularity
Language:Python 110
sregistry
singularityhub / sregistry
server for storage and management of singularity images
containers management registry singularity singularity-containers singularityhub
Language:JavaScript 103
netreconlab / parse-hipaa
HIPAA & GDPR compliant ready parse-server with postgres/mongo, parse-hipaa-dashboard. Compatible with ParseCareKit
parse-server postgres postgis backend-as-a-service graphql parse-dashboard hipaa mongodb baas mbaas cloud healthcare gdpr carekit hacktoberfest docker singularity
Language:JavaScript 97
JuliaContainerization / SimpleContainerGenerator.jl
Create container images for using Julia packages (especially useful in environments without Internet access)
containers docker julia-language julia-package-compiler julia-packages offline singularity static-compilation
Language:Julia 94
biocorecrg / master_of_pores
Nextflow pipeline for analysis of direct RNA Nanopore reads
docker nanopore-analysis-pipeline nanopore-sequencing nextflow nextflow-pipeline singularity
Language:Nextflow 88
giesselmann / nanopype
Snakemake pipelines for nanopore sequencing data archiving and processing
docker nanopore pipeline singularity snakemake-pipelines workflow
Language:Python 88
Barsonax / Singularity
A extremely fast ioc container for high performance applications
duality ioc ioc-container dependency-injection csharp di inversion-of-control inversionofcontrol ioc-framework singularity dependency-injection-container dotnet netcore netstandard di-container net
Language:C# 76
singularityhub / singularity-compose
orchestration for singularity containers (under development)
container-orchestration singularity singularity-compose
Language:Python 70
connectomemapper3
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.
bids bidsapp dmri fmri connectome bids-apps pipelines chuv brain parcellation python eeg docker singularity
Language:HTML 68
github-ci
singularityhub / github-ci
An example GitHub Action (CI) to build a Singularity container
container github-ci singularity singularity-ci
Language:Singularity 65
genepi / nf-gwas
A nextflow pipeline to perform state-of-the-art genome-wide association studies.
gwas regenie nextflow slurm singularity imputation
Language:Nextflow 61
PangzeCheung / SingDiffusion
[CVPR 2024] Tackling the Singularities at the Endpoints of Time Intervals in Diffusion Models
cvpr2024 diffusion-model singularity text-to-image-generation diffusers
Language:Python 58
singularity-cli
singularityhub / singularity-cli
streamlined singularity python client (spython) for singularity
cli client containers hacktoberfest singularity singularity-python
Language:Python 55
sigven / gvanno
Generic human DNA variant annotation pipeline
docker gene vep vcfanno germline variant-annotations vcf snv indels annotation-framework annotation-tool workflow singularity snvs variants disease-gene-association
Language:Python 53
vsoch / forward
Port Forwarding Utility
sherlock hpc singularity forwarding ssh-forwarding jupyter python notebook ssh
Language:Shell 51
brighill / singularity-deepin
Singularity容器运行 deepin wine 微信
wechat linux deepin deepin-wine-wechat deepin-wine singularity
Language:C 48
dirkpetersen / hpc-containers
You should offer both Podman and Apptainer with name spaces on your HPC systems
apptainer containers hpc podman rootless-containers singularity
Language:Shell 48
dentist
a-ludi / dentist
Close assembly gaps using long-reads at high accuracy.
genome-assembly gap-filling pacbio long-reads close-assembly-gaps snakemake damapper cluster daligner dub singularity docker bioinformatics
Language:D 47
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.
distributed-computing workflows java python c workflow-management-system pipeline-framework hpc docker singularity slurm
Language:Java 47
dz333n / Singularity-OS
Microsoft Research Singularity RDK 2.0 Source
csharp dotnet microsoft operating-system research singularity
Language:C# 47
JasonYangShadow / lpmx
A novel composable rootless container system
docker rootless rootless-container container-linux unionfs fakeroot fakechroot docker-image singularity
Language:Go 46