kwellswrasman/atac_chip repository overview

⁠General docker for ATAC-seq and ChIP-seq analysis

This image contains bowtie2, featureCounts, fastqc, cutadapt, macs3, hmmratac and bbtools used for ATAC-seq and ChIP-seq analysis. All packages and versions can be found within the pixi.toml and pixi.lock files.

Recipes for this package can be found on github

• V1⁠

This has been written to work with Snakemake pipelines

• V1 ATAC-seq⁠
• V1 ChIP-seq⁠

⁠Downloading the image

To download, the image, you can simply run

docker pull kwellswrasman/atac_chip:v1

⁠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 atac_chip:v1 ./

⁠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 atac_chip:v1 ./

Then run within the image

docker run -it --mount type=bind,source="$(pwd)",target=/app/atac_chip atac_chip:v1 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 atac_chip

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

exit
docker build -t atac_chip:v1 ./

⁠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.

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

apptainer build atac_chip_v1.sif Singularity