Storing pathogen-host interactions data from different source DBs including PHI-base into Ensembl Interspecies interactions DB
A registry file with the urls of the interspecies_interactions_db, the ncbi_tax, and meta_db database servers specified.
A .csv file from the source_DB from which the interactions are sourced.
A .obo file with the descritption of the controlled terms used to describe different aspects of the interactions (optional)
init_pipeline.pl Bio::EnsEMBL::EGPipeline::PipeConfig::Map_interspecies_interactions_conf \
-pipeline_url $EHIVE_URL
-reg_file $REGISTRY
-source_db $SOURCE_DB
-hive_force_init 1
-inputfile $INPUT_FILE
-queue_name production
-fails_folder $FAILS_PATH
| option | default value | meaning |
|---|---|---|
-reg_file |
Different format than the one previously used in the perl eHive pipeline. This one centralises the url DB details for some databases that the pipeline is going to access. Specifically: interactions_db_url, ncbi_tax_url and meta_db_url | |
-inputfile |
path to the prepared PHI-base current snapshot | |
-obo_file |
optional path to any .obo file containing controlled vocabulary or ontologies used to describe the interactions properties | |
-source_db |
name of the sourceDB from where we are importing data.ie.- 'PHI-base' | |
-fails_folder |
path to the folders logging the entries that have failed at any stage of the pipeline |
N.B. The pipeline is still under construction. The first block (populating interactions to our interactionsDB) is operational but will undergo further modifications. A second part to this pipeline will extrapolate new interactions using Ensembl resources.