DNAnexus applet for the stepcount Python package

Scripts, configuration files, and instructions to build a DNAnexus applet wrapping the Python package stepcount (https://github.com/OxWearables/stepcount) for use on the DNAnexus platform.

Prerequisites

• Python 3.8 or higher
• The DNAnexus dx toolkit: pip install dxpy

The following shows how to use Anaconda to satisfy the above prerequisites (you can use any Python environment manager):

1. Download & install Miniconda (light-weight version of Anaconda).
2. (Windows) Once installed, launch the Anaconda Prompt.
3. Create a virtual environment:

   conda create -n dxpy python=3.9 pip

   This creates a virtual environment called dxpy with Python version 3.9 and Pip.
4. Activate the environment:

   conda activate dxpy

   You should now see (dxpy) written in front of your prompt.
5. Install dxpy:

   pip install dxpy

You are all set! You have created an environment called dxpy, containing the DNAnexus package dxpy. The next time that you want to use dxpy, open the Anaconda Prompt and activate the environment (step 4: conda activate dxpy). If you see (dxpy) in front of your prompt, you are ready to go!

Read the DNAnexus Quickstart to learn the core "dx" commands: https://documentation.dnanexus.com/getting-started/cli-quickstart. TL;DR:

• Use dx login to login to your DNAnexus account (username and password are the same as with the web browser).
• Most DNAnexus commands are basically Unix commands prefixed with "dx". For example:
  • dx ls to list files
  • dx cd to navigate folders
  • dx mkdir to create new folders
  • dx rm to remove files
  • dx mv to move/rename files
  • ...

Building the applet

1. Clone this repository:

   git clone https://github.com/OxWearables/dnanexus-stepcount.git

2. Navigate to cloned folder:

   cd dnanexus-stepcount/

3. Build the asset required by the applet:

   dx build_asset stepcount-asset

   Note: This might take 10-15 minutes!

   When the build finishes, it will display an asset ID at the end (something like record-Gx3Z650JyBV1f4p5fV7Xp4ZQ). Copy this ID. If you missed it, you can re-read it using dx describe stepcount-asset.

4. Open the file stepcount/dxapp.json and search for the field "assetDepends":

   "assetDepends": [
     {
       "id": "record-..."
     }
   ]

   Replace "record-..." with the ID you copied from the previous step. Save and exit.

5. Finally, build the applet:

   dx build stepcount
   

Running the applet

To begin, download a sample accelerometer file:

https://wearables-files.ndph.ox.ac.uk/files/data/samples/ax3/tiny-sample.cwa.gz

and upload it to your DNAnexus project: dx upload tiny-sample.cwa.gz

Now you can run stepcount on the uploaded sample file:

dx run stepcount -iinput_file=tiny-sample.cwa.gz

Note: This might take 5-10 minutes!

After the run finishes, you should see an "outputs/" folder in your DNAnexus project. You can check with dx tree outputs/ which should look like this:

outputs/
└── tiny-sample
    ├── tiny-sample-Bouts.csv.gz
    ├── tiny-sample-Daily.csv.gz
    ├── tiny-sample-DailyAdjusted.csv.gz
    ├── tiny-sample-Hourly.csv.gz
    ├── tiny-sample-HourlyAdjusted.csv.gz
    ├── tiny-sample-Info.json
    ├── tiny-sample-Minutely.csv.gz
    ├── tiny-sample-MinutelyAdjusted.csv.gz
    ├── tiny-sample-Steps.csv.gz
    ├── tiny-sample-Steps.png
    └── tiny-sample-StepTimes.csv.gz

Troubleshooting

• Error: ('destination project is in region aws:xx-xxxx-x but "regionalOptions" do not contain this region. Please, update your "regionalOptions" specification',)
  • Solution: Open stepcount/dxapp.json and search for the "regionalOptions" field:

    "regionalOptions": {
        "aws:eu-west-2": {
            ...
        }
    }

    Change "aws:eu-west-2" to your project region as indicated in your error message.