Environment variables

There are several environment variables that are also useful to setup. They are not required but can make some things easier.

The GWAS_SOURCE_DATA_ROOT environment variable

If you have a bunch of files that you wish to normalise. Then you can set the GWAS_SOURCE_DATA_ROOT environment variable. This then gives you the option of using relative paths to those files within your XML metadata file. This is useful if you ever alter your directory paths, as you do not need to edit any written XML files. It is not essential, you can choose to use absolute paths to your GWAS data within the XML file and then this environment variable is not used.

The GWAS_DEST_DATA_ROOT environment variable

This works in a similar way to the GWAS_SOURCE_DATA_ROOT environment variables but is the location of the normalised data. Again, you can choose to ignore it and use absolute paths. However, if you are creating a repository of GWAS data then it may be useful.

The GWAS_ID_FILE environment variable

This should contain a path to an ID file that is used to generate study and analysis integer identifiers. This is described in detail in the metadata documentation.