GitHub topics: singularity-container

Repositories

NYU-Molecular-Pathology/LG-PACT

NYU Langone Genome PACT (Genome Profiling of Actionable Cancer Targets) targeted exome sequencing analysis pipeline.

Language: Nextflow - Size: 2.16 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 8 - Forks: 1

apptainer/apptainer

Apptainer: Application containers for Linux

Language: Go - Size: 39.8 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 1,323 - Forks: 148

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: 11 days ago - Pushed at: over 2 years ago - Stars: 2,570 - Forks: 427

singularityhub/singularity-catalog

The Singularity Community Catalog of Singularity* recipe files.

Language: Singularity - Size: 215 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 11 - Forks: 2

ReproNim/neurodocker

Generate custom Docker and Singularity images, and minimize existing containers

Language: Python - Size: 8.35 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 342 - Forks: 97

aws-samples/cfd-on-singularity-with-aws-parallelcluster

Example of how to run OpenFOAM on a Singularity container through AWS ParallelCluster.

Language: Shell - Size: 170 KB - Last synced at: 4 days ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 1

ehw-fit/tf-approximate

Approximate layers - TensorFlow extension

Language: C - Size: 6.11 MB - Last synced at: 13 days ago - Pushed at: about 2 months ago - Stars: 27 - Forks: 12

WEHI-ResearchComputing/container-recipes

Container recipes created by the RCP team

Language: Roff - Size: 38.1 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

CSCfi/csc-env-matlab

Containerized MATLAB and MATLAB Parallel Server environment for HPC clusters at CSC.

Language: Shell - Size: 226 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 1

kaczmarj/apptainer-in-docker

Apptainer in Docker!

Language: Dockerfile - Size: 24.4 KB - Last synced at: about 2 months ago - Pushed at: 6 months ago - Stars: 46 - Forks: 10

bencardoen/singularity_slurm_cuda

Example on how to get started with Singularity and CUDA on a SLURM cluster

Language: Shell - Size: 214 KB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 6 - Forks: 0

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: about 1 month ago - Pushed at: almost 3 years ago - Stars: 8 - Forks: 1

manuparra/singularitycontainers-on-m1-arm64

This is a repository containing a ready-to-use environment for singularity in arm64 (Apple M1).

Language: Python - Size: 237 KB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 17 - Forks: 3

singularityhub/singularity2docker

convert a singularity image back to Docker, full circle! #containerfriends

Language: Shell - Size: 28.3 KB - Last synced at: about 2 months ago - Pushed at: about 5 years ago - Stars: 24 - Forks: 9

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: about 2 months ago - Pushed at: 3 months ago - Stars: 18 - Forks: 0

pydicom/dicom-containers

singularity and Docker containers to easily get started with common dicom tools

Language: Dockerfile - Size: 31.3 KB - Last synced at: 2 months ago - Pushed at: about 5 years ago - Stars: 22 - Forks: 1

rbberger/vim-singularity-syntax

Vim Syntax Highlighting for Singularity files

Language: Vim script - Size: 3.91 KB - Last synced at: 2 months ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 3

Serka-M/mmlong2-lite

Lightweight bioinformatics pipeline for microbial genome recovery

Language: Python - Size: 1.18 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 9 - Forks: 3

legend-exp/legend-prodenv

LEGEND Data Production Environment

Language: Python - Size: 77.1 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 8

singularityhub/sregistry-cli

Singularity Global Client for container management

Language: Python - Size: 2.64 MB - Last synced at: 29 days ago - Pushed at: almost 2 years ago - Stars: 15 - Forks: 17

ncar-xdev/repo2apptainer

Repo2apptainer: Wrapper around repo2docker producing Jupyter enabled Apptainer/Singularity images.

Language: Python - Size: 59.6 KB - Last synced at: 7 days ago - Pushed at: 2 months ago - Stars: 5 - Forks: 0

E4S-Project/e4s-cl

Container manager for E4S

Language: Python - Size: 2 MB - Last synced at: 5 months ago - Pushed at: 10 months ago - Stars: 15 - Forks: 4

marcelzwiers/fmriprep_sub

Utilities for using fmriprep on the DCCN compute cluster

Language: Python - Size: 21.4 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1

felixdittrich92/Document_Scanner

this repository contains utils for post processing scanned documents and classify any kind of document for the given labels

Language: Python - Size: 51.9 MB - Last synced at: 2 days ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 4

bencardoen/SPECHT.jl

SPECHT is a Julia implementation of a contrastive weakly supervised object detection and identification method for fluorescence microscopy.

Language: Julia - Size: 10.4 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 4 - Forks: 0

bids-apps/ndmg

BIDS app for NeuroData's MRI to Graphs pipeline

Language: Dockerfile - Size: 71.3 KB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 5 - Forks: 8

radudaia/yocto-build-containers

Language: Makefile - Size: 1.95 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

qiyang-ustc/ALPS_SIF

Singularity def file and old version source file to produce a MPI-support, compiled singularity image. Easy to follow and include.

Language: Makefile - Size: 41.5 MB - Last synced at: 3 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

bencardoen/singularity_julia

Template definition file for Singularity RO containers with Julia and user package embedded.

Size: 18.6 KB - Last synced at: 2 months ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0

hpcng/nomad-driver-singularity

HashiCorp Nomad driver plugin - Singularity

Language: Go - Size: 4.44 MB - Last synced at: 6 months ago - Pushed at: about 2 years ago - Stars: 25 - Forks: 8

singularityhub/paraview-visualizer

Singularity container recipes to run the paraview visualizer

Size: 29.3 KB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 4 - Forks: 1

fanurs/data-analysis-e15190-e14030

Data analysis for the experiment E15190-E14030 at the National Superconducting Cyclotron Laboratory (NSCL), currently known as the Facility for Rare Isotope Beams (FRIB). This experiment aims to constrain the nuclear equation of state with heavy ion collisions at intermediate energies.

Language: Python - Size: 51.1 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 2 - Forks: 0

locastre/autoseg_container_boilerplate

Boilerplate example code for adapting home-brewed deep learning models to use with the CERR Auto-Segmentation Pipeline.

Language: Python - Size: 21.5 KB - Last synced at: 12 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1

singularityhub/.github

community wide code of conduct and other documents

Language: HTML - Size: 5.86 KB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

supercontainers/isc-tutorial

ISC 2023 -- Getting Started with Containers on HPC

Language: C++ - Size: 106 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 6

soichih/docker-tensorflow-bigred2

Tensorflow Container for IU BigRed 2

Language: Shell - Size: 2.93 KB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0

sci-f/apps

Modular application recipes for the Scientific Filesystem (SCIF)

Language: CSS - Size: 3.18 MB - Last synced at: 2 months ago - Pushed at: about 5 years ago - Stars: 3 - Forks: 3

kinow/cylc-singularity

Singularity containers for Cylc

Language: Roff - Size: 3.91 KB - Last synced at: 2 months ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 1

BartoszBartmanski/SingularityCARNIVAL

Repository for CARNIVAL singularity images based on Ubuntu 20.04.

Language: R - Size: 31.3 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

Reidmen/LegacyFEniCSonHabrok

Legacy FEniCS with Singularity

Language: Dockerfile - Size: 43 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

VUIIS/hello-world-MCR

Test code for generating containers using Singularity and Matlab compiler.

Language: MATLAB - Size: 225 KB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 2

mcw-rcc/mitograph

Singularity container for MitoGraph.

Language: Singularity - Size: 1000 Bytes - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

maxemil/ALE-pipeline

nextflow pipeline to automate analysis using ALE (https://github.com/ssolo/ALE)

Language: Python - Size: 162 KB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 1

FluidNumerics/research-computing-cluster

Imaging Scripts, Terraform IAC, and Documentation for the RCC

Language: Python - Size: 16.3 MB - Last synced at: 3 days ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

ranwez/MACSE_V2_PIPELINES

This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.

Language: Shell - Size: 4 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 21 - Forks: 8

maxemil/PhyloMagnet

screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics

Language: Nextflow - Size: 2.34 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 11 - Forks: 4

icaoberg/singularity-r-base-biocmanager

Singularity recipe for r-base + BiocManager

Language: Shell - Size: 1.95 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

gavinf97/Nextflow_AntiSMASH

Custom Nextflow scripts for microbiome assembly and AntiSMASH BGC analyses. Based around microbiome assemblers: Megahit & MetaSpades

Language: Nextflow - Size: 1.86 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

xiaozhah/Wine

wine in Docker & Singularity

Language: Dockerfile - Size: 55.7 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

haavee/jiveplot

Python based plotting package for CASA MeasurementSet

Language: Python - Size: 2.37 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 11 - Forks: 9

leosfan/fastq2dcc

Install the GeoMxNGSPipeline_Linux_2.0.0.16 tool from Nanostring/illumina to docker container, and convert it to Singularity.

Size: 3.91 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

roboticsleeds/isaac-orbit-container

Singularity container for Isaac Sim and Isaac Orbit with ROS Noetic.

Language: Shell - Size: 28.3 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

NucciTheBoss/vscode_roar Fork of dp2ski/vscode_aci 📦

The Roar supercomputer's implementation of VSCode

Language: Lua - Size: 34.2 KB - Last synced at: 7 days ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

NucciTheBoss/openfoam8_roar Fork of drewpolasky/openfoam8_aci

The Roar supercomputer's implementation of OpenFoam8

Language: Lua - Size: 42 KB - Last synced at: 7 days ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

sghignone/alpine-bioperl

Bioperl 1.7.7 containers based on alpine linux

Language: Dockerfile - Size: 8.79 KB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

saravanabalagi/singularity_tensorflow

Singularity tensorflow containers for research and development

Language: Shell - Size: 59.6 KB - Last synced at: 2 months ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 1

ArangoGutierrez/Singularity-on-Nomad

The Singularity on Nomad tutorial documents how to deploy Singularity on Nomad.

Language: Shell - Size: 173 KB - Last synced at: 2 months ago - Pushed at: over 7 years ago - Stars: 10 - Forks: 1

mmore500/mwe-singularity-checkpoint

A minimal working example of DMTCP checkpoint-restart inside a Singularity container.

Language: Shell - Size: 10.7 KB - Last synced at: about 1 month ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 0

singularityhub/singularity-ci

example builders for Singularity images using continuous integration

Size: 486 KB - Last synced at: about 2 months ago - Pushed at: almost 6 years ago - Stars: 9 - Forks: 2

richelbilderbeek/singularity_examples

Examples of how to use Singularity on Travis CI

Language: Shell - Size: 34.2 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

GiancarloPaoletti/PBS_qsub_gridsearch

Simple bash script to launch gridsearch qsub jobs on PBS

Language: Shell - Size: 12.7 KB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 0

singularityhub/singularity.lang

xml syntax file for formatting Singularity recipes in gedit

Language: Vim script - Size: 413 KB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 8

sci-f/container.scif

example scientific filesystem to assess metrics across different solutions to a single problem, printing "Hello World"

Language: Jupyter Notebook - Size: 7.82 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

ecr-cluster/tensor-comprehensions

Singularity Reciepe files for Facebook's Tensor Comprehensions tools

Size: 5.86 KB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

vsoch/singularity-nginx

web application to serve (simple) singularity images

Language: Python - Size: 228 KB - Last synced at: 3 months ago - Pushed at: about 8 years ago - Stars: 3 - Forks: 0

pkerbs/RIFTT

Robust identification of fusion genes in tumor transcriptomes.

Language: R - Size: 3.27 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

AlexKurek/LOFAR-containers

Singularity containers related to LOFAR

Language: Shell - Size: 21.5 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

saravanabalagi/singularity_imagemagick

Singularity container for imagemagick with GNU Parallel

Language: Shell - Size: 3.91 KB - Last synced at: 26 days ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

evchambers/singularity_containers

Collection of personal singularity container image definition files

Size: 8.79 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

asadprodhan/phyloTree

Bayesian phylogenetic analysis

Language: Nextflow - Size: 34.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

dtrudg/clair-singularity

Scan Singularity container images using a Clair server

Language: Python - Size: 157 KB - Last synced at: 6 days ago - Pushed at: about 3 years ago - Stars: 16 - Forks: 2

lab42open-team/deco

This repository contains exemplary workflow using programming tools and libraries for data rescue of historical biodiversity data. These tools combine OCR and text mining approaches to retrieve valuable information like species, functional traits and environments.

Language: R - Size: 45.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1