The aim of the RODEOS (Raw Omics Data accEss and Organisation System) system is to facilitate the management and access to Omics raw mass data (e.g., genomics or proteomics data). The system itself is based on the iRODS ecosystem:
iRODS for mass data storage and meta data management,
Metalnx as a graphical user interface to iRODS, and
Davrods for WebDAV based access to the data.
This is the documentation for the data ingest (aka data import) subsystem. That is, for the import of data into iRODS employing the irods_capability_automated_ingest (ICAI) library.
This documentation provides the following information:
the implemented logic / workflow,
the installation of the ingest services (that are based on Celery as ICAI is based on Celery),
the configuration the module using environment variables, and
how to properly call the importa via ICAI.
Where necessary, it provides hints on the configuration of external software such as Redis (an indirect dependency through Celery). However, for an overview of the “super” system RODEOS itself and the individual external libraries, please see the corresponding documentation.