We have been having also been having this issue, we get empty TopHat output
files. This is happening on two instances that were started within the past
three weeks on the cloud.


Cheers,
Mo Heydarian





---------- Forwarded message ----------
From: 吳正華 <joh...@ibms.sinica.edu.tw>
Date: Fri, Oct 12, 2012 at 11:12 PM
Subject: [galaxy-dev] Empty TopHat output
To: galaxy-dev@lists.bx.psu.edu


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****

-------------------------------------------------------------****

PhD Student****

Academia Sinica****

** **

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