Hi all:

After updating our local galaxy installation to the latest build last week, I found that when tophat finished its execution, all its output files showed empty in the history.

However, I could execute the exact same command via shell and got correct tophat output files.

It seemed that something went wrong when galaxy tried to copy tophat output files to galaxy databases/file.

Did anyone encounter the same problem? How could I fix this problem?

Thanks a lot.

Best

John Wu

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PhD Student

Academia Sinica