kwellswrasman/rnaseq_general repository overview

⁠General docker for RNA-seq analysis

This image contains STAR, featureCounts, fastqc, cutadapt, and bbtools used for RNA-seq analysis. All packages and versions can be found within the pixi.toml and pixi.lock files on github.

The recipe for this image can be found in a github repo:

• V1⁠
• V2⁠ - updated to no longer rely on anaconda

This image can be used in my RNA-seq Snakemake pipeline

• V1⁠
• V2⁠

⁠Downloading the image

To download, the image, you can simply run

docker pull kwellswrasman/rnaseq_general:v2

⁠Set up docker image

You can directly build this package on docker with the provided lock file by building from this directory.

docker build -t rnaseq_general:v2 ./

⁠Generate lock file (optional and unnecessary if the lock file exists)

If the lock file isn't present and you would like to generate it, first run the build but stop before the pixi install step (comment out all lines).

docker build -t rnaseq_general:v2 ./

Then run within the image

docker run -it --mount type=bind,source="$(pwd)",target=/app/rnaseq_general rnaseq_general:v2 sh

Within the image, run

pixi install

This will install the packages and generate a lock file. Copy the lock file to your main directory

cp pixi.lock rnaseq_general

Now exit out of the image, uncomment the full docker file, and rebuild

exit
docker build -t rnaseq_general:v2 ./

⁠Set up on Singularity/Apptainer

To build the singularity image, copy the Singularity file to your server. Update this with the appropriate version of the docker image. Update the create_sif.sh script to your specifications and submit the job. An image will generated that has already run the shell_hook.sh script and should work out of the box.

The Singularity file contains

Bootstrap: docker
From: kwellswrasman/rnaseq_general:v2

%environment
    # This will be sourced in all runs
    . /shell-hook.sh

%runscript
    # This is the command run when you call the container
    exec "$@"

If you don't want to submit the job, you can run in your terminal

apptainer build rnaseq_general_v2.sif Singularity