Pre-annotation Dockerized Pipeline for the ICTUSnet Project

Previous considerations

/full/path/to/your/input/data is your input directory that should be as below format:

data
├── file1.txt
├── file2.txt
└── ...

/full/path/to/your/output/datashould be an empty directory to put the .ann files that ictusnet docker container will generate. Being at HOME Diretory is highly recommended.

Make sure docker is installed in your system.

Build the docker image, assuming Docker is a non-root user:

bash build-docker.sh

Run the docker container, assuming Docker is a non-root user:

Note: Run the below script with two arguments: one path for TXT directory as an input and one path for ANN directory as an output.

bash run-docker.sh /full/path/to/your/input/data /full/path/to/your/output/data

For building the Singularity image, once the Docker one has been built (since it is converted using https://github.com/singularityhub/docker2singularity), assuming Singularity is installed and Docker is a non-root user, run:

bash build-singularity.sh

Run singularity image:

Note: Run the below script with two arguments: one path for TXT directory as an input and one path for ANN directory as an output.

bash run-singularity.sh /full/path/to/your/input/data /full/path/to/your/output/data

This docker image is available online at docker hub: https://hub.docker.com/r/bsctemu/ictusnet