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javild edited this page Sep 19, 2014 · 17 revisions

Preliminars

CellBase comes with a Python program to download all the data sources required for building the databases and with a Java command line interface (CLI) for building the database, you will need at least Java 7. After the installation you should have a directory with this structure: ... ...

Download data sources

You can find the Python script at...

Building CellBase

Once we have downloaded the data we can build the Data Models for MongoDB by executing:

Tu run the Java CLI you must execute:

java -jar lib/cellbase-build-3.1.0.jar --build

Installing the database

Using REST web services

Preliminars

CellBase comes with a command line interface (CLI) is written in Java, you will need at least Java 7 for running the CellBase CLI. After the installation you should have a cellbase/cellbase-build/installation-dir/ directory with:

/tmp/cellbase/cellbase-build/installation-dir/ ├── bin │   ├── cosmic │   │   └── cosmic_mutations.sh │   ├── ensembl-scripts │   │   ├── DB_CONFIG.pm │   │   ├── gene_extra_info_cellbase.pl │   │   ├── protein_function_prediction_matrices.pl . . . . . . . . . │   ├── genome-fetcher │   │   ├── CHECKSUMS │   │   ├── DB_CONFIG.pm │   │   ├── genome-fetcher.py . . . . . . . . . │   ├── obsolete │   │   ├── cellbase-builder.py │   │   └── genome_info.pl │   └── protein │   └── uniprot_spliter.pl ├── cellbase-installer.py ├── example │   ├── BasicTest.gvf │   ├── BasicTest.Json │   ├── Escherichia coli.owl │   ├── Homo_sapiens_incl_consequences_1000.gvf │   └── Homo_sapiens_incl_consequences_1000.Json ├── libs │   ├── cellbase-build-3.1.0.jar │   ├── cellbase-core-3.1.0.jar │   ├── cellbase-mongodb-3.1.0.jar . . . . . . . . . ├── mongodb-scripts │   ├── conserverd_region-indexes.js │   ├── create-biouser.js │   ├── drugbank-indexes.js . . . . . . . . . └── run_cellbase.sh

Tu run the CLI you must execute:

java -jar lib/cellbase-build-3.1.0.jar --build

Download data

Go to CellBase folder:

cd cellbase/cellbase-build/installation-dir/bin/genome-fetcher

./genome-fetcher.py -s "Homo sapiens" --sequence 1 --gene 1 --variation 1 -o /tmp

This will download the data files into /tmp folder

Generating the JSON data

Go to:

cd cellbase/cellbase-build/installation-dir/

and execute CellBase CLI, for building genome sequence collection:

java -jar libs/cellbase-build-3.1.0.jar --build genome-sequence 
 --fasta-file /tmp/homo_sapiens/sequence/<file.fa.gz> -o /tmp/

For building gene collection:

java -jar libs/cellbase-build-3.1.0.jar --build gene 
 --indir /tmp/homo_sapiens/gene 
 --fasta-file /tmp/homo_sapiens/sequence/<file.fa.gz> -o /tmp/

For building variation collections:

java -jar libs/cellbase-build-3.1.0.jar --build variation 
 --indir /tmp/homo_sapiens/variation -o /tmp/

General

Tutorials

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