Docker_kr-colab_locator

Docker container for locator NN. See: https://github.com/kr-colab/locator.git

Use with Docker

Download the Dockerfile

(you should also download Docker Desktop)

Create an image with the Dockerfile. Open terminal (or similar) and run the following:

docker build -t locator .

You must be inside of the directory containing the Dockerfile for this to work.

See image in you Docker Desktop app.

Click the RUN! button on the right side; name the container (optional).

Click the >_ button which will open the container in terminal.

Find the scripts directory.

ls scripts

Use with Singularity (Apptainer)

Load module first if necessary. module load singularity

Download docker image to be run with singluarity.

singularity pull locator.sif docker://finchnsnps/locator:locator_v2

Open container as a shell with singularity.

singularity shell --cleanenv locator.sif

Find locator scripts directory under /

ls /locator/scripts

Test container

See https://github.com/kr-colab/locator.git for details about test data, output files, parameters, visualization, and interpretation.

Make output directory

mkdir out/test

Use test data to test the container

In docker:

python scripts/locator.py --vcf data/test_genotypes.vcf.gz --sample_data data/test_sample_data.txt --out out/test/test

In singularity

python /locator/scripts/locator.py --vcf /locator/data/test_genotypes.vcf.gz --sample_data /locator/data/test_sample_data.txt --out out/test/test