I'm trying to run ensembl-vep with Docker from a python code on a Linux server. When the following Docker command runs
docker run -t -i -v $HOME/vep_data:/opt/vep/.vep ensemblorg/ensembl-vep
the command line is changed (it enters the Docker image), and the script pauses, until I exit the image by pressing
ctrl+D. The next command in the script is
vep --cache --offline --format vcf --vcf --force_overwrite \ --input_file input/input.vcf \ --output_file output/output.vcf'''
and now that the script is out of the image the input folder that's specified in the command is not recognized.
Is there a way to use the Docker image without entering the image command line interface?
I used a Docker image before and this scenario did not happen, yet I couldn't find what made the difference between the two commands.