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 three base directories :

• EXTERNAL_DATA_BASE

This is the base directory of all external Data sources - 
A directory is created for each downloaded source. 

Example:
EXTERNAL_DATA_BASE=/data/external

Then we will have -
- /data/external/ensembl -- based directory for all Ensembl releases downloaded 
- /data/external/wormbase -- based directory for all Wormbase releases downloaded 
....

• SCRATCH_DATA_BASE

This is the base directory to store unzipped datasets - 
A directory for each downloaded source will be found here. 

Example:
SCRATCH_DATA_BASE=/data/scratch

Then we will have -
- /data/scratch/ensembl -- based directory for all Ensembl releases downloaded 
- /data/scratch/wormbase -- based directory for all Wormbase releases downloaded 
....

• LOGS_BASE

All the logs generated from download scripts will be stored under LOGS_BASE/data_downloads

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