.. _ggd_cli_page:


GGD Commands
============

[:ref:`Click here to return to the home page <home-page>`]

**To see and/or search for data packages available through GGD, see:** :ref:`Available data packages <recipes>`

.. important::

    If you use GGD, please cite the `Nature Communications GGD paper <https://www.nature.com/articles/s41467-021-22381-z>`_


The ggd command line interface (cli) has multiple tools for data access and local management. Below you can find a short
description of each tool, as well as links to specific pages about each. 

Tabs for each tool are also available on the left tab bar.  

+----------------------------------------------------+--------------------------------------------------------------------+
|    Command                                         | Description                                                        |
+====================================================+====================================================================+
| :ref:`ggd search <ggd-search>`                     |  Search for a ggd data package                                     |
+----------------------------------------------------+--------------------------------------------------------------------+
| :ref:`ggd predict-path <ggd-predict-path>`         | Predict the file path of a data package that has not been          |
|                                                    | installed yet (Good for workflows like Snakemake)                  |
+----------------------------------------------------+--------------------------------------------------------------------+
| :ref:`ggd install <ggd-install>`                   | Install ggd data package(s)                                        |
+----------------------------------------------------+--------------------------------------------------------------------+
| :ref:`ggd uninstall <ggd-uninstall>`               | Uninstall a ggd data package(s)                                    |
+----------------------------------------------------+--------------------------------------------------------------------+
| :ref:`ggd list <ggd-list>`                         | List the installed data packages (in a specific environment)       |
+----------------------------------------------------+--------------------------------------------------------------------+
| :ref:`ggd get-files <ggd-get-files>`               | get the files for an installed ggd package                         |
+----------------------------------------------------+--------------------------------------------------------------------+
| :ref:`ggd pkg-info <ggd-pkg-info>`                 | Show a specific ggd package's info                                 |
+----------------------------------------------------+--------------------------------------------------------------------+
| :ref:`ggd show-env <ggd-show-env>`                 | Show the ggd specific environment variables                        |
+----------------------------------------------------+--------------------------------------------------------------------+
| :ref:`ggd make-recipe <ggd-make-recipe>`           | Create a ggd recipe from a bash script                             | 
+----------------------------------------------------+--------------------------------------------------------------------+
| :ref:`ggd make-meta-recipe <ggd-make-meta-recipe>` | Create a ggd meta-recipe from a single or group of script          | 
+----------------------------------------------------+--------------------------------------------------------------------+
| :ref:`ggd check-recipe <ggd-check-recipe>`         | Check/test a ggd recipe                                            | 
+----------------------------------------------------+--------------------------------------------------------------------+



Command links:

.. toctree::
   :maxdepth: 2

   ggd-search
   install
   predict-path
   uninstall
   list
   list-file
   pkg-info
   show-env
   make-recipe
   make-metarecipe
   check-recipe