Package: genomehubs
AboutGenomeHubs comprises a set of tools to parse index and search and display genomic metadata, assembly features and sequencing status for projects under theEarth BioGenome Projectumbrella that aim to sequence all described eukaryotic species over a period of 10 years.Genomehubs builds on legacy code that supported taxon-oriented databases of butterflies & moths (lepbase.org), molluscs (molluscdb.org), mealybugs (mealybug.org) and more. Genomehubs is now search-oriented and positioned to scale to the challenges of mining data across almost 2 million species.The first output from the new search-oriented GenomeHubs is Genomes on a Tree (GoaT,goat.genomehubs.org), which has been opublised in: Challiset 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.18658.1The goat.genomehubs.org website is freely available with no logins or restrictions, and is being widely used by the academic community and especially by the Earth BioGenome Project to plan and coordinate efforts to sequence all described eukaryotic species.The core GoaT/Genomehubs components are available as a set of Docker containers:GoaT UIA bundled web server to run a GoaT-specific instance of the GenomeHubs UI, as used atgoat.genomehubs.org.Usagedockerpullgenomehubs/goat:latestdockerrun-d--restartalways\--netnet-es-p8880:8880\--user$UID:$GROUPS\-eGH_CLIENT_PORT=8880\-eGH_API_URL=https://goat.genomehubs.org/api/v2\-eGH_SUGGESTED_TERM=Canidae\--namegoat-ui\genomehubs/goat:latestGenomehubs UIA bundled web server to run an instance of the GenomeHubs UI, such asgoat.genomehubs.org.Usagedockerpullgenomehubs/genomehubs-ui:latestdockerrun-d--restartalways\--netnet-es-p8880:8880\--user$UID:$GROUPS\-eGH_CLIENT_PORT=8880\-eGH_API_URL=https://goat.genomehubs.org/api/v2\-eGH_SUGGESTED_TERM=Canidae\--namegh-ui\genomehubs/genomehubs-ui:latestGenomehubs APIA 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 atgoat.genomehubs.org/api-docs.Usagedockerpullgenomehubs/genomehubs-api:latestdockerrun-d\--restartalways\--netnet-es-p3000:3000\--user$UID:$GROUPS\-eGH_ORIGINS="https://goat.genomehubs.org null"\-eGH_HUBNAME=goat\-eGH_HUBPATH="/genomehubs/resources/"\-eGH_NODE="http://es1:9200"\-eGH_API_URL=https://goat.genomehubs.org/api/v2\-eGH_RELEASE=$RELEASE\-eGH_SOURCE=https://github.com/genomehubs/goat-data\-eGH_ACCESS_LOG=/genomehubs/logs/access.log\-eGH_ERROR_LOG=/genomehubs/logs/error.log\-v/volumes/docker/logs/$RELEASE:/genomehubs/logs\-v/volumes/docker/resources:/genomehubs/resources\--namegoat-api\genomehubs/genomehubs-api:latest;Genomehubs CLIcommand line tool to process and index genomic metadata for GenomeHubs. Used to build and update GenomeHubs instances such as Genomes on a Treegoat.genomehubs.org.Usagedockerpullgenomehubs/genomehubs:latestParse [NCBI datasets](https://www.ncbi.nlm.nih.gov/datasets/) genome assembly metadata:dockerrun--rm--network=host\-v`pwd`/sources:/genomehubs/sources\genomehubs/genomehubs:latestbash-c\"genomehubs parse \
            --ncbi-datasets-genome sources/assembly-data \
            --outfile sources/assembly-data/ncbi_datasets_eukaryota.tsv.gz"Initialise a set of ElasticSearch indexes with [NCBI taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy/) data for all eukaryotes:dockerrun--rm--network=host\-v`pwd`/sources:/genomehubs/sources\genomehubs/genomehubs:latestbash-c\"genomehubs init \
            --es-host http://es1:9200 \
            --taxonomy-source ncbi \
            --config-file sources/goat.yaml \
            --taxonomy-jsonl sources/ena-taxonomy/ena-taxonomy.extra.jsonl.gz \
            --taxonomy-ncbi-root 2759 \
            --taxon-preload"Index assembly metadata:dockerrun--rm--network=host\-v`pwd`/sources:/genomehubs/sources\genomehubs/genomehubs:latestbash-c\"genomehubs index \
            --es-host http://es1:9200 \
            --taxonomy-source ncbi \
            --config-file sources/goat.yaml \
            --assembly-dir sources/assembly-data"Fill taxon attribute values across the tree of life:dockerrun--rm--network=host\-v`pwd`/sources:/genomehubs/sources\genomehubs/genomehubs:latestbash-c\"genomehubs fill \
            --es-host http://es1:9200 \
            --taxonomy-source ncbi \
            --config-file sources/goat.yaml \
            --traverse-root 2759 \
            --traverse-infer-both"Related projectsSome GenomeHubs components are hosted in separate open source repositories (all under MIT licenses), including:BlobToolKitInteractive quality assessment of genome assemblies.Explore analysed public assemblies atblobtoolkit.genomehubs.org/viewGoaT CLIA command line interface for GoaT.The GoaT CLI builds URLs to query the Goat API, removing some of the complexity of theGoaT API. for the end user.Changelog2.0.0 (2020-07-02)First release on PyPI.