kwellswrasman/fastq_screen repository overview

⁠fastq-screen docker

The recipes for this image can be found on github

• V1⁠

This is built to work with Snakemake pipelines

• RNA-seq⁠
• ATAC-seq⁠
• ChIP-seq⁠

Following installation guide here⁠

⁠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 fastq_screen: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 fastq_screen:v1 ./

Then run within the image

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

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

exit
docker build -t fastq_screen: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 fastq_screen_v1.sif Singularity

⁠Set up once the image is built

Once this is built, within the docker image run

fastq_screen --get_genomes

And save the genomes to a helpful location. Then update the fastq_screen.conf and keep with the docker image. Pass this using

fastq_screen --conf /path/to/fastq_screen.conf sample1.fastq sample2.fastq