Table 1 A catalog of GGD tools available via the command-line interface.
From: Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data
GGD CLI tool | Description of functionality |
|---|---|
ggd search | Search for available data packages based on a search term(s) with genomic specific filters. |
ggd predict-path | Predict the installed file path for a file in a data package that has not been installed. (Useful for workflows like Snakemake). |
ggd install | Install one or more data package(s) to a specific Conda environment on a user’s system. |
ggd uninstall | Uninstall a data package from a Conda environment from a user’s system. |
ggd list | Report the installed data packages within a specific Conda environment (similar to conda list). |
ggd get-files | List the file(s) associated with an installed package on a user’s system. |
ggd pkg-info | Retrieve the data package information of an installed data package on a user’s system. |
ggd show-env | Display the GGD specific environment variables for the installed packages in a specific Conda environment on a user’s system. |
ggd make-recipe | Make a GGD data recipe that can be added to the GGD recipe ecosystem. The tool will transform a simple Bash script into a ggd data recipe. |
ggd make-meta-recipe | Make a GGD data meta-recipe that can be added to the GGD recipe ecosystem. The tool will transform a single or group of scripts into a GGD data meta-recipe, which can be used to install ID specific data packages. |
ggd check-recipe | Transform a GGD recipe that has been created from running ‘make-recipe’ into a GGD data package and test the validity of the data package. |
