Running

You run the ingest from the directory $SOURCE to the destination collection $DEST as follows. Use the papropriate path to the handler module that you want to use.

/opt/rodeos-ingest-env/bin/python \
    -m irods_capability_automated_ingest.irods_sync \
    start \
        --event_handler rodeos_ingest.genomics.illumina.bcl \
        --job_name rodeos-ingest-$(date +%Y-%m-%d_%H-%M-%S) \
         \
        --exclude_file_name ".*_MANIFEST_*.txt"  \
        -- \
        $SOURCE \
        $DEST

Please refer to the ICAI documentation (or the output when including --help) for more information.

The following handler modules are provided.

module	data type
rodeos_ingest.genomics.illumina.bcl	Illumina run folders
rodeos_ingest.genomics.illumina.fastq	FASTQ demultiplexing results