Repos Main Configuration

This file contains global configs and should be modified after running the setup.sh script and before running any other script.

Make sure you have full permissions to create/delete on those base directories.

Package Base Directories

You only need to modify the following four base directories :

• SOFTWARE_BASE

The Path to global  bin, include, lib directories. This is where the bin, 
includes, and lib of each tool will be copied after the install. 
This base directory is equivalent to /usr/local and should be 
included in your environment PATH.

For example:
 SOFTWARE_BASE=/opt/software 

If you have full permission on /usr/local in your system, 
then set SOFTWARE_BASE=/usr/local

• EXTERNAL_SOFTWARE_BASE

This is the base directory of all the third-party tools install - 
A directory for each installed tool will be found here. 

Example:
EXTERNAL_SOFTWARE_BASE=/opt/software/external

Then we will have -
- /opt/software/external/blat -- based directory for all blat versions installed
- /opt/software/external/hisat2 -- based directory for all hisat2 versions installed
....

• LOGS_BASE

All the logs generated from the installs will be stored under LOGS_BASE

Example: LOGS_BASE=/data/logs
then logs will be under /data/logs/package_downloads

• PACKAGE_DOWNLOADS_BASE

The full path to where package_downloads is installed.

Example:
PACKAGE_DOWNLOADS_BASE=/home/bioadmin/package_downloads