#

singularity

Here are 496 public repositories matching this topic...

apptainer / singularity

Open

Emit progress information during SIF creation

8

mikegray commented Jun 13, 2019

Version of Singularity:

3.0.3

Expected behavior

Some progress or update information during the creation of the SIF file.

Actual behavior

During "Creating SIF file..." step, the console does not produce any visible output for the user - but does create the resulting file eventually.

Steps to reproduce behavior

I was executing a few “larger” builds through the bui

Read more

Enhancement ImageBuilding good first issue

Open

Documentation of -S and -W are meaningless

4

Open

refactor `singularity help help` text

3

Find more good first issues

nextflow

nextflow-io / nextflow

A DSL for data-driven computational pipelines

docker groovy hello aws cloud bioinformatics pipeline nextflow hpc reproducible-research workflow-engine slurm pipeline-framework sge singularity reproducible-science dataflow singularity-containers

Updated May 15, 2022
Groovy

NVIDIA / hpc-container-maker

HPC Container Maker

docker hpc containers singularity

Updated May 11, 2022
Python

Azure / batch-shipyard

Simplify HPC and Batch workloads on Azure

docker serverless hpc azure containers gpu mpi slurm nfs singularity azure-batch azure-functions glusterfs rdma infiniband batch-processing windows-containers

Updated Oct 18, 2021
Python

getpopper / popper

Open

example: add a CI pipeline for gradle

1

ivotron commented Jun 19, 2020

Add an example workflow in the examples/gradle/ folder that exemplifies how to make use of Popper to create a CI pipeline for java projects that use gradle as their build system. The image used by the workflow can be the official one.

Read more

good first issue

Open

doc: write "overview" section

1

Open

cli: colorize output

9

apptainer / apptainer

Apptainer: Application containers for Linux

linux science hpc containers singularity singularity-container rootless-containers apptainer

Updated May 13, 2022
Go

glotzerlab / hoomd-blue

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

python docker simulation gpu cuda molecular-dynamics singularity monte-carlo-simulation particle-system conda-forge hard-particle hoomd-blue

Updated May 14, 2022
C++

singularityhub / docker2singularity

A docker image for converting docker images to singularity images.

docker docker-image singularity singularity-images

Updated Apr 22, 2022
Shell

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

docker bioinformatics pdb protein-structure singularity python-bindings scientific-computing openbabel plip

Updated Apr 5, 2022
Python

Sarek

SciLifeLab / Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

docker workflow bioinformatics pipeline genomics nextflow cancer somatic-variants reproducible-research containers next-generation-sequencing singularity badge reproducible-science travis-link somatic germline scilifelab gitter-badge germline-variants gitter-link scilifelab-link nextflow-link nbis-link ngi-link

Updated Jan 27, 2020
Nextflow

sylabs / singularity-cri

The Singularity implementation of the Kubernetes Container Runtime Interface

kubernetes hpc containers singularity cri singularity-cri

Updated Dec 29, 2020
Go

StaPH-B / docker-builds

📦

🐳 Dockerfiles and documentation on tools for public health bioinformatics

docker dockerfiles bioinformatics containers singularity

Updated May 13, 2022
Dockerfile

sregistry

singularityhub / sregistry

server for storage and management of singularity images

registry containers management singularity singularity-containers singularityhub

Updated Apr 23, 2022
JavaScript

sylabs / wlm-operator

Singularity implementation of k8s operator for interacting with SLURM.

kubernetes hpc slurm singularity k8s kubernetes-operator

Updated Dec 29, 2020
Go

giesselmann / nanopype

Snakemake pipelines for nanopore sequencing data archiving and processing

docker workflow nanopore pipeline singularity snakemake-pipelines

Updated Feb 2, 2022
Python

x11vnc / x11vnc-desktop

Docker/Singularity image for Ubuntu with X11 and VNC

docker html5 ubuntu websocket x11 singularity novnc vnc

Updated May 16, 2022
Python

JuliaContainerization / SimpleContainerGenerator.jl

Create container images for using Julia packages (especially useful in environments without Internet access)

docker offline containers julia-language singularity julia-packages julia-package-compiler static-compilation

Updated Dec 25, 2021
Julia

biocorecrg / master_of_pores

Nextflow pipeline for analysis of direct RNA Nanopore reads

docker nextflow singularity nanopore-sequencing nextflow-pipeline nanopore-analysis-pipeline

Updated Jan 12, 2022
HTML

bdusell / singularity-tutorial

Tutorial for using Singularity containers

container cuda singularity pytorch cudnn

Updated Oct 1, 2020

Barsonax / Singularity

Sponsor

A extremely fast ioc container for high performance applications

ioc csharp dotnet dependency-injection singularity netcore di-container inversion-of-control ioc-container net netstandard duality di dependency-injection-container ioc-framework inversionofcontrol

Updated Sep 14, 2020
C#

singularity-hpc

singularityhub / singularity-hpc

Open

Add tests for wrappers

vsoch commented Mar 17, 2022

Singularity HPC newly added support for wrappers:

https://singularity-hpc.readthedocs.io/en/latest/getting_started/user-guide.html?highlight=wrappers#wrapper-scripts

But we didn't properly (thoroughly) test them. This addition should add a new test_wrappers.py script under shpc/tests that goes through the process of:

installing without a wrapper (confirming no wrapper directory is gene

Read more

good first issue

singularityhub / singularity-compose

orchestration for singularity containers (under development)

singularity container-orchestration singularity-compose

Updated Mar 29, 2022
Python

github-ci

singularityhub / github-ci

An example GitHub Action (CI) to build a Singularity container

container singularity singularity-ci github-ci

Updated Feb 22, 2022
Singularity

JasonYangShadow / lpmx

A novel composable rootless container system

docker docker-image singularity fakeroot unionfs container-linux fakechroot rootless rootless-container

Updated Apr 30, 2022
Go

singularity-cli

singularityhub / singularity-cli

streamlined singularity python client (spython) for singularity

cli client containers singularity hacktoberfest singularity-python

Updated Mar 29, 2022
Python

dgruber / wfl

A Simple Way of Creating Job Workflows in Go running in Processes, Containers, Tasks, Pods, or Jobs

go macos linux docker kubernetes golang workflow hpc containers workflow-engine singularity processes k8s high-throughput

Updated May 8, 2022
Go

gaoxifeng / Robust-Hexahedral-Re-Meshing

Hex-mesh simplification and optimization

singularity simplification hexahedral-mesh global-structure

Updated Jun 10, 2018
C++

dentist

a-ludi / dentist

Close assembly gaps using long-reads at high accuracy.

docker bioinformatics snakemake cluster singularity dub pacbio dentist genome-assembly daligner long-reads gap-filling gaps low-complexity-regions snakemake-workflow close-assembly-gaps damapper snakemake-cluster

Updated Mar 1, 2022
D

vsoch / forward

Sponsor

Port Forwarding Utility

python ssh jupyter hpc notebook sherlock singularity forwarding ssh-forwarding

Updated Mar 25, 2022
Shell

vsoch / scif

Sponsor

scientific filesystem: a filesystem organization for scientific software and metadata

docker metadata organization containers container singularity standard scientific-filesystems

Updated Feb 24, 2020
Python

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