Getting empty files when upload

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Getting empty files when upload

Erwan Delage

Hello dear galaxy developpers,

I'm facing a weird bug when trying to upload files in Galaxy. 

When I want to upload, let's say for example a csv file, the dataset turns green but the file is empty. I checked in the galaxy datasets directory, the file is here but empty.

And this happens only when configuring Galaxy to work with SGE on a cluster, not when running "locally".

I did take a look at the script and I found that if I replace the call to shutil.move( dataset.path, output_path ) by calling shutil.copy(dataset.path, output_path) at the end of the add_file function, then it works.

Both Galaxy temp and dataset directories are on the same partition, and when I try from a cluster execution node to manually do a shutil.move from the temp directory to the dataset directory with the galaxy user, it works well.

Any idea of what could go wrong here ?



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