On Mar 12, 2012, at 2:23 PM, Fields, Christopher J wrote:

> You can change the default location of tmp files by modifying the 
> environment; we ran into this with samtools directly dumping temp sort files 
> to a local node, causing the job to shut down.  Setting TMPDIR worked for me.

Hi Chris,

Thanks for pointing this out, I've added it to the cluster wiki page:

http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Galaxy_Configuration

--nate

> 
> chris
> 
> On Mar 11, 2012, at 5:10 PM, Dorset, Daniel C wrote:
> 
>> Hi Luciano,
>> 
>> I had a similar problem with our local instance of Galaxy. In our case, the 
>> /tmp directory was filling up, causing the job to abort. We had Galaxy 
>> running on a partition with tons of disk space, but the partition on which 
>> /tmp was located had substantially less free disk space. Try running the 
>> "df" command from the Linux command line. If you don't know how to interpret 
>> its output, let me know.
>> 
>> Certain tasks that run on behalf of Galaxy, like gzip for decompressing 
>> large datasets, will store intermediate temporary data in /tmp instead of a 
>> subdirectory within your Galaxy installation.
>> 
>> Let me know if that solves your issue,
>> 
>> Dan
>> ________________________________________
>> 
>> Message: 1
>> Date: Sat, 10 Mar 2012 17:25:38 -0600
>> From: Luciano Cosme <cosme.sim...@gmail.com>
>> To: Galaxy-dev <galaxy-dev@lists.bx.psu.edu>
>> Subject: [galaxy-dev] Error while uploading
>> Message-ID:
>>       <camasfsjdm0udcivqk7p-mpijr8ualxe0zx7szug4upsqj_n...@mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>> 
>> Hi,
>>  I uploaded 11 files today (1 to 2Gb compressed files) to my local
>> instance without a problem (as admin). Then I got this error message below
>> and it get stuck at "This dataset is uploading" and I could not upload the
>> last files. Is there anything I can do to solve it? What I notice is that I
>> can still upload small files, before I concatenate them. I have 15 time
>> points and some of them have up to 20 files, so it is easier to concatenate
>> them and them upload.
>> Thank you.
>> 
>> Luciano
>> 
>> 
>> 
>> 
>> 
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> 
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