Main GENIE detailed error reporting

Installation

Clone this repository and navigate to the directory:

git clone git@github.com:Sage-Bionetworks/genie-main-details.git
cd genie-main-details

If running without Docker, install all required R packages:

R -e 'renv::restore()'

If running with Docker, build the containter:

docker build -t genie-main-details .

Synapse credentials

Cache your Synapse personal access token (PAT) as an environmental variable:

export SYNAPSE_AUTH_TOKEN={your_personal_access_token_here}

Usage without Docker

To display the command line interface:

Rscript genie-main-details.R -h

The command line interface will display as follows:

Usage: genie-main-details.R [options]


Options:
        -u, --upload
                Upload results to Synapse; otherwise, write locally

        -v, --verbose
                Output script messages to the user.

        -h, --help
                Show this help message and exit

Example run:

Rscript genie-main-details.R -v -u

Usage with Docker

To display the command line interface:

docker run -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN --rm genie-main-details -h

The command line interface will display as follows:

Usage: genie-main-details.R [options]


Options:
        -u, --upload
                Upload results to Synapse; otherwise, write locally

        -v, --verbose
                Output script messages to the user.

        -h, --help
                Show this help message and exit

Example run:

docker run -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN --rm genie-main-details -v -u