Displaying 1 to 11 from 11 results

singularity - Singularity: Application containers for Linux

  •    Go

Singularity is an open source container platform designed to be simple, fast, and secure. Singularity is optimized for EPC and HPC workloads, allowing untrusted users to run untrusted containers in a trusted way. Check out who is using Singularity and some use cases of Singularity on our website.

Singularity - Grids without limits

  •    CSS

Singularity is a next generation grid framework built from the ground up to be responsive. What makes Singularity different? Well, a lot of things. Singularity is based on internal ratios instead of context based which allows for better gutter consistency across breakpoints. Ratio based math also allows for non-uniform grids in any unit you want to use. Layout on the web has changed significantly since Scott's first push back on March 7, 2012. First came Flexbox, then CSS Grid. CSS Grid provides layout functionality that covers all of Singularity's usecases and then quite a few more that we were never really able to support.

nextflow - A DSL for data-driven computational pipelines

  •    Groovy

With the rise of big data, techniques to analyse and run experiments on large datasets are increasingly necessary. Parallelization and distributed computing are the best ways to tackle this kind of problem, but the tools commonly available to the bioinformatics community traditionally lack good support for these techniques, or provide a model that fits badly with the specific requirements in the bioinformatics domain and, most of the time, require the knowledge of complex tools or low-level APIs.

Singularity RDK

  •    

The Singularity Research Development Kit (RDK) is a Shared Source project based on the Singularity research project out of Microsoft Research. The Singularity RDK is available for academic non-commercial use only. Singularity is a research project focused on the construction...




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

  •    Nextflow

Previously known as the Cancer Analysis Workflow (CAW), Sarek is a workflow tool designed to run analyses on WGS data from regular samples or tumour / normal pairs, including relapse samples if required. It's built using Nextflow, a bioinformatics domain specific language for workflow building. Software dependencies are handled using Docker or Singularity - container technologies that provide excellent reproducibility and ease of use. Singularity has been designed specifically for high-performance computing environments. This means that although Sarek has been primarily designed for use with the Swedish UPPMAX HPC systems, it should be able to run on any system that supports these two tools.

hpc-container-maker - HPC Container Maker

  •    Python

HPC Container Maker (HPCCM) generates container specification files, either Dockerfiles or Singularity recipe files, based on a "recipe." A recipe specifies the series of steps to be performed when building a container. The recipe format is described elsewhere. Recipes provide more portable, higher level building blocks that separate the concerns of choosing what to include in a container from the low level details of container specification. At first glance, the idea of specifying a container in a new, non-native format may not seem worthwhile. For small, simple containers, this is probably true. However, for larger, more complex containers, there are 3 good reasons to use Container Maker recipes.

scif - scientific filesystem: a filesystem organization for scientific software and metadata

  •    Python

This module will provide tools for generating and interacting with scientific filesystems, optimized for use on a host or inside a container. This code is licensed under the Affero GPL, version 3.0 or later LICENSE.

forward - Sherlock Port Forwarding Utility

  •    Shell

Forward sets up an sbatch script on your cluster resource and port forwards it back to your local machine! Useful for jupyter notebook and tensorboard, amongst other things. The folder sbatches contains scripts, organized by cluster resource, that are intended for use and submission. It's up to you to decide if you want a port forwarded (e.g., for a jupyter notebook) or just an instruction for how to connect to a running node with your application.


hack17-tutorial - Nextflow basic tutorial for newbie users

  •    Nextflow

This repository contains the tutorial material for the Nextflow workshop.

singularity-cri - The Singularity implementation of the Kubernetes Container Runtime Interface

  •    Go

This repository contains Singularity implementation of Kubernetes CRI. Singularity CRI consists of two separate services: runtime and image, each of which implements K8s RuntimeService and ImageService respectively. The CRI is currently under development and passes 69/74 validation tests. Note that used test suite is taken from master branch. Detailed report can be found here.

docker2singularity - A docker image for converting docker images to singularity images.

  •    Shell

Are you developing Docker images and you would like to run them on an HPC cluster supporting Singularity? Are you working on Mac or Windows with no easy access to a Linux machine? If the pull, build, and general commands to work with docker images provided by Singularity natively do not fit your needs, docker2singularity is an alternative way to generate Singularity images. This particular branch is intended for Singularity 2.5.1, which gives you a selection of image formats to build. The containers are also available for you on Docker Hub. Note that you are able to convert easily from a folder or ext3 image using Singularity 2.4. If your choice is to develop, making changes, and then finalize, this approach is not recommended - your changes are not recorded and thus the image not reproducible.