genomehubs/easy-import repository overview

⁠EasyImport

View on Github⁠

Runs the EasyImport⁠ scripts to import data into and export files from Ensembl databases. Used both for Importing new assemblies, gene models and functional annotations into an Ensembl and for generating files for downloads and BLAST services as part of a GenomeHubs Ensembl mirror⁠.

Full documentation for EasyMirror on readme.io⁠ will be updated soon.

docker run -d \
           --name easy-import-melitaea_cinxia_core_32_85_1 \
           --link genomehubs-mysql \
           -v ~/demo/genomehubs-mirror/import/conf:/import/conf \
           -v ~/demo/genomehubs-mirror/import/data:/import/data \
           -v ~/demo/genomehubs-mirror/download/data:/import/download \
           -v ~/demo/genomehubs-mirror/blast/data:/import/blast \
           -e DATABASE=melitaea_cinxia_core_32_85_1 \
           -e FLAGS="-e -j -i" \
           easy-import

FLAGS are used to control which EasyImport scripts are run, in this example -e runs the export_sequences.pl script to generate sequence files for downloading and BLAST, -j runs the export_json.pl script to generate json files used by the assembly-stats⁠ and codon-usage⁠ visualisations on species home pages and -i runs the index_database.pl script to provide search.