README.rst

pl-simpledsapp

Table of Contents

• Abstract
• Description
• Usage
  • Arguments
  • Run
• Development
• Examples

Abstract

A simple ChRIS ds app demo.

Description

simpledsapp basically does an explicit copy of each file in an input directory to the output directory, prefixing an optional string to each filename.

Usage

python simpledsapp.py
    [-h] [--help]
    [--json]
    [--man]
    [--meta]
    [--savejson <DIR>]
    [-v <level>] [--verbosity <level>]
    [--version]
    <inputDir>
    <outputDir>
    [--prefix <PREFIX>]
    [--ignoreInputDir]
    [--sleepLength <SECONDS>]
    [--dummyInt <INT>]
    [--dummyFloat <FLOAT>]

Arguments

[-h] [--help]
If specified, show help message and exit.

[--json]
If specified, show json representation of app and exit.

[--man]
If specified, print (this) man page and exit.

[--meta]
If specified, print plugin meta data and exit.

[--savejson <DIR>]
If specified, save json representation file to DIR and exit.

[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.

[--version]
If specified, print version number and exit.

<inputDir>
Input directory.

<outputDir>
Output directory.

[--prefix <PREFIX>]
If specified, append this prefix to resulting output files.

[--ignoreInputDir]
If specified, ignore the input dir completely.

[--sleepLength <SECONDS>]
If specified, time to sleep before performing plugin action.

[--dummyInt <INT>]
If specified, this is a dummy (not used) input integer parameter.

[--dummyFloat <FLOAT>]
If specified, this is a dummy (not used) input float parameter.

Getting inline help is:

docker run --rm fnndsc/pl-simpledsapp simpledsapp --man

Run

You need you need to specify input and output directories using the -v flag to docker run.

docker run --rm -u $(id -u)                             \
    -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
    fnndsc/pl-simpledsapp simpledsapp                        \
    /incoming /outgoing

Development

Build the Docker container:

docker build -t local/pl-simpledsapp .

Run unit tests:

docker run --rm local/pl-simpledsapp nosetests

Examples

docker run --rm -u $(id -u)

-v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing fnndsc/pl-simpledsapp simpledsapp /incoming /outgoing --prefix lolo