genomehubs/genomehubs-api

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By genomehubs

Updated 3 months ago

Open source bundled web server to run an instance of the GenomeHubs API

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Data Science
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GenomeHubs API

An open-source bundled web server to run an instance of the GenomeHubs API. The GenomeHubs API underpins all search functionality for Genomes on a Tree (GoaT) goat.genomehubs.org. OpenAPI documentation for the GenomeHubs API instance used by GoaT is available at goat.genomehubs.org/api-docs.

About

GenomeHubs API has been published in: Challis et al. 2023, Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life. Wellcome Open Research, 8:24 doi:10.12688/wellcomeopenres.18658.1

This container is updated using an automated build from github.com/genomehubs/genomehubs

All underlying code is freely available under an MIT license.

The GoaT API (deployed as a GenomeHubs API instance) is freely available with no logins or restrictions and is widely used by the academic community, especially the Earth BioGenome Project. GoaT API can be queried directly or via the Goat UI or GoaT CLI.

Usage

docker pull genomehubs/genomehubs-api:latest

docker run -d \
    --restart always \
    --net net-es -p 3000:3000 \
    --user $UID:$GROUPS \
    -e GH_ORIGINS="https://goat.genomehubs.org null" \
    -e GH_HUBNAME=goat \
    -e GH_HUBPATH="/genomehubs/resources/" \
    -e GH_NODE="http://es1:9200" \
    -e GH_API_URL=https://goat.genomehubs.org/api/v2 \
    -e GH_RELEASE=$RELEASE \
    -e GH_SOURCE=https://github.com/genomehubs/goat-data \
    -e GH_ACCESS_LOG=/genomehubs/logs/access.log \
    -e GH_ERROR_LOG=/genomehubs/logs/error.log \
    -v /volumes/docker/logs/$RELEASE:/genomehubs/logs \
    -v /volumes/docker/resources:/genomehubs/resources \
    --name goat-api \
    genomehubs/genomehubs-api:latest;

Docker Pull Command

docker pull genomehubs/genomehubs-api