Versions Compared
Key
- This line was added.
- This line was removed.
- Formatting was changed.
Load Data
Please, note that beforeAfter you have generated the JSON data files (see Building the CellBase database), you can now load them in your Mongo database.
Configure Database Credentials
Before loading the data into the database
CellBase configuration.json, your settings.xml file must have been appropriately configured indicating the database host names, ports, user and password.
CellBase code is open-source and freely available at https://github.com/opencb/cellbaseHere are the expected parameters:
name | default |
---|---|
CELLBASE.DB.MONGODB.HOST | localhost:27017 |
CELLBASE.DB.USER | <empty> |
CELLBASE.DB.PASSWORD | <empty> |
CELLBASE.SERVER.REST.PORT | 9090 |
Load JSON files into MongoDB
Use the CellBase CLI to load the data models:. For
example,
to
load
all
human
(GRCh37)
data
models
from
the
/tmp/data/cellbase/v4/homo_sapiens_grch37/mongodb/
created
in
section
"Build
Data
Models",
into
the
cellbase_hsapiens_grch37_v4
database
and creating the indexes as indicated in the.js
scripts within cellbase/cellbase-app/app/mongodb-scripts/
, run::
Code Block |
---|
cellbase/build/bin$ ./cellbase.sh load -d variation --database cellbase_hsapiens_grch37_v4 -i /mnt/data/downloads/cellbase/v4/homo_sapiens_grch37/mongodb/ -L debug -Dmongodb-index-folder=/home/cafetero/appl/dev/cellbase/cellbase-app/app/mongodb-scripts/ |
Please, note that the whole loading and indexing process may need ~24h to complete, depending on the available hardware.
After successful load of all data, the corresponding database shall look like:
$ mongo mongodb-dev/cellbase_hsapiens_grch37_v4 MongoDB shell version: 3.0.9 connecting to: mongodb-dev/cellbase_hsapiens_grch37_v4clinical_variants > show collections; clinical_variants conservation gene genome_info genome_sequence metadata protein protein_functional_prediction protein_protein_interaction regulatory_region repeats variation variation_functional_score
Table of Contents:
Table of Contents | ||
---|---|---|
|