No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded.  Every time we tried uploading, it finished with no errors but was empty. Turning the nfs caching off fixed this. 

From: Iry Witham <Iry.Witham@jax.org>
Date: Thursday, August 14, 2014 9:34 AM
To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: [galaxy-dev] Upload file not working with new install

Hi Team,

I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool.  When I attempt to use it it just sits and spins.  No data gets uploaded.  I have looked through the universe.wsgi.ini file and cannot find anything there that stands out.  Can you point me to a possible solution?

Thanks,
Iry

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