The first step to creating a CellBase instance is to download the data files. Download can be done through the CellBase CLI:
cellbase/build/bin$ ./cellbase.sh download
The following option is required: -d, --data
Usage: cellbase.sh download [options]
Options:
-a, --assembly STRING Name of the assembly, if empty the first assembly in configuration.json will be used [GRCh37]
--common STRING Directory where common multi-species data will be downloaded, this is mainly protein and expression
data [<OUTPUT>/common]
-C, --config STRING CellBase configuration.json file. Have a look at
cellbase/cellbase-core/src/main/resources/configuration.json for an example
* -d, --data STRING Comma separated list of data to download: genome, gene, gene_disease_association, variation,
variation_functional_score, regulation, protein, conservation, clinical and . 'all' to download
everything
-h, --help Display this help and exit [false]
-L, --log-level STRING Set the logging level, accepted values are: debug, info, warn, error and fatal [info]
-o, --output STRING The output directory, species folder will be created [/tmp]
-s, --species STRING Name of the species to be downloaded, valid format include 'Homo sapiens' or 'hsapiens' [Homo
sapiens]
-v, --verbose BOOLEAN [Deprecated] Set the level of the logging [false]
A number of datasets can be downloaded as indicated by the built-in documentation: `genome, gene, gene_disease_association, variation, variation_functional_score, regulation, protein, conservation, clinical`. An option `all` is implemented for the `--data` parameter to allow downloading all data by a single command. Some datasets (`genome` and `gene`) need the ENSEMBL perl API to be properly installed in order to be fully downloaded. Please note: all data can be downloaded, built and loaded in the database without the ENSEMBL API but some bits may be missing, e.g. gene xrefs.
For example, to download all human (GRCh37) data from all sources and save it into the `/tmp/data/cellbase/v4/` directory, run:
`cellbase/build/bin$ ./cellbase.sh download -a GRCh37 --common /tmp/data/cellbase/v4/common/ -d all -o /tmp/data/cellbase/v4/ -s hsapiens`
**Please note:** ensure you are located within the `cellbase/build/bin` directory before running the `download` command. Some perl scripts that use the ENSEMBL API may not be properly run otherwise.
Please, also note that heavy files will be downloaded and therefore the time needed for completion may vary between minutes and even hours.
If download was successful, you can proceed to building the json objects that should be loaded into the corresponding database: [[Build & Load Data]].