2. Tutorial

2.1. Convert the files for an entry to additional formats

Run the following command to convert the files for an entry to additional formats such as BioPAX, MATLAB/Octave, and XPP:

ENTRY_DIR=/path/to/directory-for-entry
biomodels-qc convert "$ENTRY_DIR"

2.2. Validate an entry

Run the following command to validate an entry of the BioModels database:

ENTRY_DIR=/path/to/directory-for-entry
biomodels-qc validate "$ENTRY_DIR"

2.3. Using the Docker image

Run the following commands to use the BioModels-QC Docker image to execute the same conversion and validation operations.

Convert the files for an entry to additional formats:

ENTRY_DIR=/path/to/directory-for-entry
docker run \
    --mount type=bind,source="$ENTRY_DIR",target=/biomodels-entry \
    --interactive \
    --tty \
    --rm \
    ghcr.io/biosimulations/biomodels_qc \
        convert \
            /biomodels-entry

Validate an entry:

ENTRY_DIR=/path/to/directory-for-entry
CONTAINER_TEMP_DIR=$(mktemp --directory)
docker run \
    --mount type=bind,source="$ENTRY_DIR",target=/biomodels-entry \
    --volume /var/run/docker.sock:/var/run/docker.sock \
    --mount type=bind,source="$CONTAINER_TEMP_DIR",target=/tmp \
    --env TEMP_DIR_HOST_PATH=$CONTAINER_TEMP_DIR \
    --interactive \
    --tty \
    --rm \
    ghcr.io/biosimulations/biomodels_qc \
        validate \
            /biomodels-entry