npg_irods

Overview

This repository is the home of application code used by NPG to manage data and metadata in WSI iRODS.

It includes:

• Tools for managing data in iRODS from various analysis platforms, including:

  • Illumina sequencing instruments
  • PacBio sequencing instruments
  • BioNano optical mapping instruments

• General purpose tools for bulk data management in iRODS

For each platform there are scripts to upload data to iRODS, annotate it with metadata describing its origin and set data access permissions. There are further scripts to update metadata and access permissions in response to upstream changes.

The core metadata used by NPG to annotate analysis results in iRODS are described in a separate repository

Building and testing

This repository has dependencies declared in Build.PL, which must be installed prior to building. There is a working example of this in the CI workflow run-tests.yml.

An iRODS server is required for the tests. The iRODS configuration environment variable used by the tests is intentionally different from iRODS' default to reduce the risk of accidentally running tests against a different iRODS server than intended. The environment variable WTSI_NPG_iRODS_Test_IRODS_ENVIRONMENT_FILE must be set to the path of a client iRODS environment JSON configuration file corresponding to the test server. See the iRODS documentation for more information about this file.

Once this is done, tests may be run with the command:

perl Build.PL
./Build test