Set Up File Provisioning Plugins
================================

.. note:: Currently, the Dockstore CLI's GS plugin does not support files that are located in `requester-pays <https://cloud.google.com/storage/docs/requester-pays>`__ buckets.

File provisioning plugins can be used to extend the Dockstore CLI to
allow for input and output files to be downloaded or uploaded to new
and/or proprietary services. By default, the Dockstore CLI tries to read
input/output files from the local filesystem and copy/hard-link to them.
If that does not work, it will look at whether any of the installed
plugins can handle the files. Finally, it will try using
`commons-vfs2 <https://commons.apache.org/proper/commons-vfs/filesystems.html>`__
to handle the files.

Generally, the Dockstore CLI downloads a default set of file
provisioning plugins, Amazon S3, Synapse, DOS, and GS when it first installs.
However, if you chose to download and
configure the CLI yourself via step 3 of Part 1 during the
`quickstart <https://dockstore.org/quick-start>`__ tutorial and did not
have a Dockstore account set up, then no file provisioning plugins will
have downloaded. To check if you have the plugins, run the command
``dockstore plugin list``. You should see something like

.. figure:: /assets/images/docs/file-provisioning-plugins.png
   :alt: file provisioning plugins

If not, run ``dockstore plugin download``.

The specification file for the plugins will be located at
``~/.dockstore/plugins.json`` by default and is created the first time
you run the command ``dockstore plugins download``. The location can be
overridden by using the key ``plugins-json-location`` in your Dockstore
config file.

Configuration for plugins can be added to your
``~/.dockstore/config``\ and is indexed by id. For example:

::

    token = <your generated by the dockstore site>
    server-url = https://www.dockstore.org/api

    # options below this are optional

    use-cache = false                           #set this to true to cache input files for rapid development
    cache-dir = /home/<user>/.dockstore/cache   #set this to determine where input files are cached (should be the same filesystem as your tool working directories)

    [dockstore-file-synapse-plugin]

    [dockstore-file-s3-plugin]
    endpoint = #set this to point at a non AWS S3 endpoint


To try an example and learn more about file provisioning, check out this
:ref:`tutorial <file-provisioning>`.

If you would like to create your own plugins, follow along
:doc:`here <developing-file-provisioning-plugins>`.

.. discourse::
    :topic_identifier: 1838