Getting started in 5 min

Preparation

Download or pull the version you want to try, you can build the application from sources executing:

mvn clean install -DskipTests

Copy the application (or the content of build folder) into the installation directory, by default and in this tutorial this is /opt/opencga

You check that all the command lines (CLIs) work fine by executing them with -h parameter, this should print the help. The CLIs are in the bin folder: opencga-admin.sh, opencga-analysis.sh and opencga.sh

Indexing a VCF file

Installing Catalog

For administering the OpenCGA installation you can use opencga-admin.sh command line. To install catalog database execute from the installation directory:

./bin/opencga-admin.sh catalog install -p

The MongoDB database host and name will be read from the ./conf/catalog-configuration.yml file by default. This CLI will create the database, the collections and all the indexes, it also creates the admin user with the specified password.

Note: you do not have to write the admin password in the CLI, this will be asked later. This password will be stored as the admin password.

Creating the user and study

By default OpenCGA is configured as private what means that only admin user can create other users. We can use the same CLI to create a user:

./bin/opencga-admin.sh users create -p -u imedina --user-email [email protected] --user-name Nacho --user-password

Again, you do not have to write the password in the command line. Two passwords are requested now, first the admin password to gain privileges (this will be remembered 2 minutes soon), second the user password (users can change this password later)

Adding and indexing a VCF file