cBioPortal
Search…
Pre-Build Steps

Get the Latest Code

Make sure that you have cloned the last code, and make sure you are on the master branch:
1
git clone https://github.com/cBioPortal/cbioportal.git
2
git checkout master
Copied!

Prepare the log4j.properties File

This file configures logging for the portal. An example file is available within GitHub:
1
cd src/main/resources
2
cp log4j.properties.EXAMPLE log4j.properties
Copied!
But you must update the following lines with paths that make sense for the systems your build should target.
1
log4j.appender.a.rollingPolicy.FileNamePattern = ${catalina.base}/logs/public-portal.log.%d.gz
2
log4j.appender.a.File = ${catalina.base}/logs/public-portal.log
Copied!

Create the cBioPortal MySQL Databases and User

You must create a cbioportal database and a cgds_test database within MySQL, and a user account with rights to access both databases. This is done via the mysql shell.
1
> mysql -u root -p
2
Enter password: ********
3
4
Welcome to the MySQL monitor. Commands end with ; or \g.
5
Your MySQL connection id is 64
6
Server version: 5.6.23 MySQL Community Server (GPL)
7
8
Copyright (c) 2000, 2015, Oracle and/or its affiliates. All rights reserved.
9
10
mysql> create database cbioportal;
11
Query OK, 1 row affected (0.00 sec)
12
13
mysql> create database cgds_test;
14
Query OK, 1 row affected (0.00 sec)
15
16
mysql> CREATE USER 'cbio_user'@'localhost' IDENTIFIED BY 'somepassword';
17
Query OK, 0 rows affected (0.00 sec)
18
19
mysql> GRANT ALL ON cbioportal.* TO 'cbio_user'@'localhost';
20
Query OK, 0 rows affected (0.00 sec)
21
22
mysql> GRANT ALL ON cgds_test.* TO 'cbio_user'@'localhost';
23
Query OK, 0 rows affected (0.00 sec)
24
25
mysql> flush privileges;
26
Query OK, 0 rows affected (0.00 sec)
Copied!
Last modified 2yr ago