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acdc_deposit

Simple repository to facilitate preparation of data prior to data transfer for the Australian Cardiovascular disease Data Commons

Usage

  1. Clone repo:
git clone https://github.com/AustralianBioCommons/acdc_deposit.git
  1. Create a directory structure for a study with ID AusDiab:
bash create_template.sh -s AusDiab

To create the directory structure in a custom destination run:

bash create_template.sh -s AusDiab -o path/to/target/dest

This will create a directory named YYYY-MM-DD_AusDiab_ACDC_Data_Transfer (where YYYY-MM-DD is the current date).

Options

  • -s STUDY_ID: The study identifier used to name the root directory. This is a required argument.
  • -o OUTPUT_DIR: Specify the output directory where the structure will be created. Default is the current directory.

Directory Structure

The script will create the following directory structure:

YYYY-MM-DD_STUDY_ID_ACDC_Data_Transfer/
├── clinical/
├── genomic/
├── imaging/
├── metabolomic/
├── proteomic/
├── study/
└── study/data_dictionaries/

Manifest File

A manifest.tsv file will be created in the root directory with the following header:

study_id	subject_id	file_path	file_name	data_category	file_size	md5_hash

License

This project is licensed under the Apache License 2.0 - see the LICENSE file for details.