I decided to test the data library suggestion that I could mount the FTP server as my data library. My files shows up in the FTP folder but not in the data libraries list.
Do you perhaps have an idea on this @martenson based on the permission discussion on Friday?
Command I ran:
docker run -p8082:80 --name Ebba2 -v monlibftp:/export/ -e "GALAXY_CONFIG_BRAND=Sunday" -e "GALAXY_CONFIG_USER_LIBRARY_IMPORT_DIR=/export/ftp" -e "GALAXY_CONFIG_USER_LIBRARY_IMPORT_DIR_AUTO_CREATION=true" -e "GALAXY_LOGGING=full" bgruening/galaxy-stable