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.
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,
> Message: 1
> Date: Sat, 10 Mar 2012 17:25:38 -0600
> From: Luciano Cosme <cosme.sim...@gmail.com>
> To: Galaxy-dev <email@example.com>
> Subject: [galaxy-dev] Error while uploading
> Content-Type: text/plain; charset="iso-8859-1"
> 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.
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Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: