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Note | ||
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We have already processed all these data and json documents are available through our FTP server for those users who wish to skip |
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this section. Download the JSON from here: http://bioinfo.hpc.cam.ac.uk/downloads/cellbase/v4/homo_sapiens_grch37/mongodb/ |
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Download data sources
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cellbase/v4/homo_sapiens_grch38/mongodb/ And follow the instructions here: Load Data |
The first step to creating a CellBase instance is to download the data files. Download can be done through the CellBase CLI:.
Code Block |
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$ cellbase/build/bin$ ./cellbase.sh download |
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data |
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genome,gene |
The --data argument is required and is a comma separated list of data types to download. See below for the full list.
Type | Data sources |
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genome |
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gene |
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variation ** |
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variation_functional_score |
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regulation |
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protein |
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conservation ** |
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clinical_variants ** |
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repeats |
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svs |
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all ** | Downloads all of the above |
See Download Sources for details on versions and available organisms.
Warning |
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** Please note that many files are very large and can take several hours to download. |
For example, to download all human (GRCh37) data from all sources and save it into the `/tmp/data/cellbase/v4/` directory, run:
Code Block |
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cellbase/build/bin$ ./cellbase-admin.sh download -a GRCh37 --common /tmp/data/cellbase/v4/common/ -d all -o /tmp/data/cellbase/v4/ |
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-s
hsapiens |
If download was successful, you can proceed to building the json objects that should be loaded into the corresponding database: [[Build & Load Data]]. Building the CellBase database