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My recommended approach is to define BOTH the root directories of data and PGE directories you need for executing PGEs defined in either your tasks.xml file, or within a .bashrc file. Next, create derived environment variables for all your specific Windows PGE needs within your PGE. This way, the Linux and Windows environment variables are passed to your batchstubs through metadata automatically.
Example implementation to look at:
Directory containing Linux/Windows configured PGE’s: https://github.com/EDRN/labcas-pipelines/tree/master/backend/workflows/proteome-pge/src/main/resources/config/tabblab
Example Win PGE file: https://github.com/EDRN/labcas-pipelines/blob/master/backend/workflows/proteome-pge/src/main/resources/config/tabblab/proteome-preprocessing.tabblab.pgeconfig.xml
Example .bashrc file (linux): https://github.com/EDRN/labcas-pipelines/blob/44871c37cf03d3484265eaacb8843ec3816e6546/backend/linux/config/src/main/conf/.bashrc
Example .bashrc file (win): https://github.com/EDRN/labcas-pipelines/blob/6338fd6a61f136ee08c725b08d8f828488b60702/backend/win/config/src/main/conf/.bashrc
Workflow Manager tasks.xml file (search for ProteomePreprocessingTabbLab): https://github.com/EDRN/labcas-pipelines/blob/master/backend/linux/workflow/src/main/conf/policy/proteomics-pipeline/tasks.xml