Running the EasyImport container

docker run --rm \
           --name easy-import-operophtera_brumata_v1_core_32_85_1 \
           --link genomehubs-mysql \
           -v ~/demo/genomehubs-import/import/conf:/import/conf \
           -v ~/demo/genomehubs-import/import/data:/import/data \
           -v ~/demo/genomehubs-import/download/data:/import/download \
           -v ~/demo/genomehubs-import/blast/data:/import/blast \
           -e DATABASE=operophtera_brumata_v1_core_32_85_1 \
           -e FLAGS="-s -p -g -e -j -i" \
           genomehubs/easy-import:latest

The environment variables (-e are most likely to need changing between runs as these specify the DATABASE to be used and FLAGS specify which scripts to run.

The easy import container must be able to access a MySQL database server, the --link option sets up a link to a docker container running MySQL and allows this container name to be given as the database host in the configuration files

Four directories are mounted in this example:

/import/conf must contain the configuration files, when exporting files from a mirrored database the database-specific configuration file is optional but database connection settings must be given in either default.ini or overwrite.ini
/import/data is used as a temporary location for downloaded and processed files and error logs for each of the EasyImport scripts, mounting this directory allows files to be reused and is useful for debugging
/import/download is the directory to which files will be exported for hosting with the h5ai container, this need only be mounted when running the export scripts.
/import/blast is the directory to which files will be exported for hosting with the SequenceServer container, this need only be mounted when running the export_sequences script.