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Command Line Interface

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javild edited this page Oct 30, 2015 · 5 revisions

Usage

The Command Line Interface is provided through the cellbase.sh executable, which can be found in the downloadable .tar.gz at build/bin/cellbase.sh or alternatively at cellbase-server/target/cellbase.sh after compiling the source code:

/tmp/cellbase/build/bin$ ./cellbase.sh 

Program:     CellBase (OpenCB)
Version:     3.2.0
Description: High-Performance NoSQL database and RESTful web services to access the most relevant biological data

Usage:       cellbase.sh [-h|--help] [--version] <command> [options]

Commands:
            download  Download all different data sources provided in the configuration.json file
               build  Build CellBase data models from all data sources downloaded
                load  Load the built data models into the database
               query  Query and fetch data from CellBase database using this command line
  variant-annotation  Annotate variants from VCF files using CellBase and other custom files
           post-load  Complements data already loaded in CellBase

There are five different commands available in the command line:

  • download
  • build
  • load
  • query
  • variant-annotation

General

Tutorials

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