parse-dbgap-application

This repository contains python scripts to parse information out of a dbGaP application PDF.

Right now, there is one script provided:

• parse_dars.py: parse the list of DARs that have been applied for in the dbGaP application PDF.

Usage

On AnVIL

See the workflow on Dockstore. To run the workflow, you will need to upload the dbGaP application PDF to a Google bucket and provide the path to the PDF as an input to the workflow. The workflow runs two steps:

1. Extract DARs into a text file.
2. Render an Rmarkdown report with basic info about the requested DARs.

Local use

• Clone the repository:

git clone https://github.com/UW-GAC/parse-dbgap-application.git

• Create a virtual environment:

python -m venv venv

• Insall requirements

pip install -m requirements.txt

• Run script

python parse_dars.py <path_to_application_pdf> <path_to_output_tsv>

Updating the docker images

docker build -t uwgac/parse-dbgap-application:<tag> .
docker push uwgac/parse-dbgap-application:<tag>