Contribute

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To see and/or search for data packages available through GGD, see: Available data packages

Important

If you use GGD, please cite the Nature Communications GGD paper

Similar to Conda and Bioconda, ggd encourages and relies on community contributions. Our vision is that ggd will become a widely used data management system in genomics and other research fields. ggd will help reduce the time it takes to find, extract, and process the necessary data for any analysis and support research reproducibility/replicability. Similar to the use of conda for package management, and Bioconda for biological software package management, ggd will become a common tool for accessing the required data for your research needs.

With the contributions and maintenance of data recipes from the research community, ggd will become a common tool for using scientific data. ggd will empower scientists to perform and analyze research data quicker and more accurately, providing a steady tool for scholarly advancement.

We invite everyone to contribute data recipes to ggd, and thus providing access to scientific data for scientists around the world.

The ggd tool has been developed to help with contributing data recipes to ggd and a few functions are provided to make this process easy. Outlined below is the steps that should be followed to create data recipe and add it to the ggd data repository.

1. Github

   • You will need a github account and a forked repository of ggd-recipes.

   • Once you have a github account and you have a forked ggd-recipes repo, you do not need to do step 1 again.

2a. Make a ggd recipe

• The following steps will outline how to create a ggd data recipe, how to test it, and how to add it to the gogetdata/ggd-recipes repo.

2b. Make a ggd meta-recipe

• The following steps will outline how to create a ggd data meta-recipe, how to test it, and how to add it to the gogetdata/ggd-recipe repo.

3. Continuous Integration testing with Circle CI

   • We use Circle CI to test all new recipes. Any recipe that passes will be officially added to the ggd repo and will be available to anyone using the ggd install tool. If it does not pass, the ggd team will work with you on getting it to pass.

Contents:

• Setting up with Github
• Contributing a ggd recipe
  • 1. Update local forked repo
  • 2. Writing a bash script to get data
  • 3. Create a ggd recipe using the ggd cli
  • 4. Build, install, and check the data recipe
  • 5. Submit the new ggd recipe to the original ggd-recipes repo
• Creating a ggd meta-recipe
  • 1. Update local forked repo
  • 2. Writing the curation script(s)
  • 3. Creating a ggd meta-recipe using the ggd cli
  • 4. Checking/Testing the new meta-recipe
  • 5. Submit the new ggd meta-recipe to the original ggd-recipes repo
  • 6. Example of the Gene Expression Omnibus (GEO) main bash script and supporting python script