This is the [pax-db.org][http://pax-db.org] species storage microservice.

Installation

Versioning

All versions are <major>.<minor>.<patch>, where major and minor follow pax-db.org versions.

License

MIT. See "LICENSE.txt".

Usage

Build js files

node --max-old-space-size=4096 build.js 

Build the image

To create the image paxdb/api-species, execute the following command:

$ docker build -t paxdb/api-species .

Run the image

$ docker run --restart=always -P -d --name paxdb_api_species paxdb/api-species

Update procedure

The process of updating to a new version is as follows:

1. update ./data/abundances (computed by data-pipeline)
2. update lib/cladogram.js
3. update ./data/orthgroups (IMPORTANT! Should include no extra taxonomic levels than required by cladogram.js)
4. update ./data/eggnog5_genome_linkout.txt (linkout to ensembl when available, otherwise to ncbi taxon browser)
5. update ./data/paxdb_uniprot_linkins_ids.tsv (generated from "BLAST_UniProt_ID" terms from STRING v11.5 protein alias file)
6. increment PAYLOAD_VERSION and update connectionString in build.js, then run it to generate lib/species.js, lib/dataset and lib/proteins