fnndsc/pl-dsdircopy repository overview

########## pl-dsdircopy ##########

Abstract

A ChRIS DS (Data Synthesis) plugin app that copies files/dirs data from one or more input sources in obj storage to an output sink.

Pre-conditions

When running this plugin from a client perspective to CUBE, note that the input directories are actually assumed to exist within obj storage, thus the value of the input directories are the prefixes within obj storage. See the wiki pages of CUBE for more information.

Run

⁠As a simple Python Application

Make sure your current working directory is dsdircopy which contains the file dsdircopy.py.

The --dir argument is a string of paths separated by commas.

.. code-block:: bash

    python3 dsdircopy.py <inputDir> <outputDir> --dir <path1, path2>

⁠Using docker run

Build the docker image using the docker build command

.. code-block:: bash

    docker build -t fnndsc/pl-dsdircopy .

Now, use the docker run command to run the docker image we created above.

Assign an "input" directory to /incoming and an output directory to /outgoing.

You also need to assign a string of paths separated by commas to the --dir argument.

.. code-block:: bash

docker run -v $(pwd):/incoming -v $(pwd)/out:/outgoing   \
        fnndsc/pl-dsdircopy dsdircopy.py            \
        --dir "chris/dir1, chris/dir2" /incoming /outgoing

The above command will do nothing as this is a sort of a ChRIS topological plugin that is not meant to be run from the command line.

Make sure that the host $(pwd)/out directory is world writable!