My team is trying to set up an instance of galaxy workflow management system that will launch jobs on our local cluster. We are involved in projects dealing with high-throughput sequencing. We then have to manage a LOT of large files (several Gb each).
When uploading files into galaxy, these files are automatically copied to a folder named "database/files" and they are also sequentially renamed (dataset1, dataset2, dataset_3 ...etc..). This name convention is independent of the fact that a file is an input/intermediary/output file.
Copying and renaming files this way is too much time consuming and makes us lose our file structure.
Is there a way to avoid this behavior and that galaxy just remember the file path instead of possessing his own copy ?
If someone here has experience with this tool, any help or useful link would be appreciated.