Dx wrapper to run the ICI uploader and upload runs to Illumina Connected Insights (ICI). This is the source code for an app that runs on the DNAnexus Platform.
This app launches the ici-uploader program and uploads a targeted folder of run data
This app may be executed as standalone or as part of an analysis pipeline.
Input files come from the output of a bioinformatics analysis pipeline.
This app requires:
- A run folder of output data - the contents depend on the workflow configuration defined by the user within ICI
- An ICI workflow ID specific to the workflow targeting your pipeline output - also defined within ICI
- An ICI API key file - a file containing your API key to access ICI programatically
- This app outputs nothing to DNANexus, but uploads data to the ICI platform
How to run this app:
Note: the run project ID is optional. If provided, the app will search that project for your data.
If not provided, the app will search the project where the app was executed (i.e. your current working project,
if the --project was not also provided to dx run).
The following example uses a TSO500 run, but this can be any type of run as long as the corresponding workflow ID is provided:
dx run app-eggd_ici_uploader/1.0.0 \
-irun_folder="project-12345abcde:/output/TSO500-241109_1148/eggd_tso500/" \
-iworkflow_id="<workflow ID string>" \
-iapi_key="<API key file>"The app requires a tar.gz of the Docker image containing the ICI uploader binary. This is bundled with the app as an app asset,
which is linked by dxapp.json. Instructions for building the asset are as follows:
Download the ICI uploader and store it in the repo directory.
docker build -t eastgenomics/ici_uploader:v<SEMANTIC_VERSION> .
mkdir -p ici-uploader-image/resources/image
docker save -o ici-uploader-image/resources/image/ici_uploader_v<SEMVER>.tar.gz
dx build_asset ici-uploader-image/