singularities

Singularity recipes for bioinformatics software. Build singularity images with these recipes (sudo required) or download/pull the images from singularity-hub.org

This repo is WORK IN PROGRESS. Feel free to try the recipes/Singularity builds, but they are not tested deeply and are in no way guaranteed to work. Proceed at your own risk.

It is somewhat modeled after https://github.com/StaPH-B/docker-builds , but with Singularity recipes instead.

Sysadmins for High Performance Cluster computers almost always favor Sinularity over Docker :) so I'm starting to learn the ways of Singularity.

Available Singularity images

Software	Version	Link
SPAdes	3.13.0	http://cab.spbu.ru/software/spades/
QUAST	5.0.0	https://github.com/ablab/quast
Lyve-SET	1.1.4f	https://github.com/lskatz/lyve-SET
SeqSero2	0.1, 1.0.0	https://github.com/denglab/SeqSero2

These Singularity images can be built if you have Singularity installed and have sudo/admin priveleges

# build an image using a recipe (called Singularity in this example)
sudo singularity build my-new-singularity-image.simg /path/to/Singularity

# download the repo
git clone https://github.com/kapsakcj/singularities.git
# another example using the SPAdes recipe
sudo singularity build my-new-spades-3.13.0-image.simg /path/to/Singularity.spades.3.13.0

These Singularity images are also available to download from singularity-hub.org if you don't have sudo priveleges (no build necessary!). The badge below is a link to the singularity-hub.org collection.

The name of the Singularity hub collection is kapsakcj/singularities and the tag is specified by the extenion of the Singularity recipe file. For example the recipe, /spades/3.13.0/Singularity.spades.3.13.0, can be downloaded like so:

# download an image like so, and name it whatever you want with the --name flag
singularity pull --name my-new-spades-3.13.0-image shub://kapsakcj/singularities:spades.3.13.0

Useful links and resources

Singularity v2.6 User guide https://www.sylabs.io/guides/2.6/user-guide/index.html
SingularityHub https://singularity-hub.org/
Excellent tutorial on Singularity (using v2.5) from Sylabs, many other links within https://github.com/Singularity-tutorial/Singularity-tutorial.github.io
How to build a container using Singularity Hub, linked to a github repo with Singularity recipes https://github.com/singularityhub/singularityhub.github.io/wiki/Build-A-Container

Tips/Tricks/Things-to-remember about Singularity [ many from Jake Garfin :) ]

Singularity automatically brings your user & group into the container with you (ie. no -u $(id -u):$(id -g) needed like in Docker)
Singularity (by default) wants to mount your entire home directory inside the container as well. Use --cleanenv and --containall to keep things separate and bring in specific directories you want with -B /local-dir:/dir-in-container
Docker images converted to Singularity that want to write to system directories owned by root aren't going to work out of the box.
If you are making a container with something that uses perl, add this to the recipe in the %environment section to prevent locale settings errors (see lyveset recipe)

%environment
    export LC_ALL=C

TO-DO

How to: Singularity
- Links to docs for installing
- How to download an image from singularity hub
- How to download an image fromm dockerhub
  - singularity pull docker://staphb/skesa
- How to take a recipe and build locally (sudo required)
- How to run a Singularity container
  - Different ways to run - singularity exec [...] or ./name-of-singularity.simg [...]
  - Mounting DIRs - default way (mount entire $HOME DIR), or way to mount a specific DIR and not entire $HOME DIR
Create SingularityHub account
- link to this repo
- create autobuilds for each recipe