Michael Hall
I am a Bioinformatics PhD student in Zam Iqbal’s lab at EMBL-EBI. I currently work on using nanopore data and genome graphs to better call variation in bacterial genomes and to compare pan-genomes.
Remote container systems
How do I access containers written by other people and/or share my own?
Michael Hall - Iqbal Group (EBI)
Singularity Hub
What is Singularity Hub?
A cloud environment that builds and stores Singularity containers from GitHub commits.
Connecting a GitHub repository
Connecting a GitHub repository
Connecting a GitHub repository
Connecting a GitHub repository
Connecting a GitHub repository
Connecting a GitHub repository
Connecting a GitHub repository
Connecting a GitHub repository
Connecting a GitHub repository
Connecting a GitHub repository
Connecting a GitHub repository
Connecting a GitHub repository
Pull a specific build from Singularity Hub
singularity run "shub://<username>/<repository>:<tag>@<hash|commit>"username="mbhall88"
repository="singularity_training"
tag="fun"
HASH="edae0eecad907e5255bd74b26b7414e0"
singularity run "shub://$username/$repository:$tag@$HASH"
# or
singularity pull --force --name fun.sif "shub://$username/$repository:$tag@$HASH"Sylabs Cloud
Sylabs Cloud
-
Container Library: official image registry for Sylabs.io
-
Remote Builder: build your image in the cloud - useful when no access to sudo
-
Keystore Service: cryptographically sign and verify images
Container Library
singularity pull --name ubuntu.sif library://library/ubuntu:18.04Use containers built by others
Remote builder
Remote builder
singularity build --remote fun.sif Singularity.fun Use the remote builder from CLI*
*Need to have a
Docker Hub
Docker Hub
Docker Hub
singularity shell docker://tensorflow/tensorflow
singularity pull docker://tensorflow/tensorflow
singularity run docker://tensorflow/tensorflow
singularity exec docker://tensorflow/tensorflowSingularity can use Docker images!!!!
Bootstrap: docker
From: tensorflow/tensorflowQuay
Quay
Container registry for Docker and rkt
Huge resource of Biocontainers!
Quay
Because there are so many containers, best to just search the tool
Quay
All Bioconda packages have a built biocontainer on quay.io
Quay
All Bioconda packages have a built biocontainer on quay.io
Quay
Quay
Quay
Quay
The way to construct these URLS is
docker://quay.io/biocontainers/<tool>:<tag>So for this example of bwa the URL would be
docker://quay.io/biocontainers/bwa:0.7.3a--h84994c4_4Quay
Quay
singularity exec docker://quay.io/biocontainers/bwa:0.7.3a--h84994c4_4 bwa mem
Remote container systems
By Michael Hall
Remote container systems
How do I access containers written by other people and/or share my own?
