Singularity Recipes
This repository is for all of my Singularity recipes and is linked to Singularity
Hub where they are built and available.
To find out more information about the different recipes, go into the directory and read through the documentation there.
Table of Contents
- Nanopore - Containers for software packages/tools relating to analysis of Oxford Nanopore Technologies sequencing data.
- Variant Calling - Containers for variant calling software.
For all recipes in the subdirectories, replace the name after the colon with the extension name of the container you want. For example
singularity pull shub://mbhall88/Singularity_recipes:nanoporeqc
This will pull the Singularity.nanoporeqc recipe. If you wanted to pull the (hypothetical) Singularity.foo container, then you would run
singularity pull shub://mbhall88/Singularity_recipes:foo
By default the containers will have a name such as mbhall88-Singularity_recipes-master-foo.simg. To name it something more succinct, run
singularity pull --name customname.simg shub://mbhall88/Singularity_recipes:foo
You don't necessarily have to pull the container onto your machine - you can execute from the Singularity Hub with
singularity exec shub://mbhall88/Singularity_recipes:mccortex mccortex31 --help
But this takes much longer to run than pulling the container and then executing it locally.
For a full list of usage examples, check out the Singularity Hub usage docs.