Thanks, Jeremy.

I updated my instance of Galaxy by the repository you provided (
https://bitbucket.org/galaxy/galaxy-dist/) and re-ran my analysis. I see
that TopHat is generating data (by monitoring the disk usage on the
Cloudman interface) again, but this time I the output file is in the error
state and the message returned is: "Job output not returned from cluster".

Any thoughts?

Thanks in advance!

Cheers,
Mo Heydarian

PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe Street
414 Hunterian
Baltimore, MD 21205



On Wed, Oct 31, 2012 at 9:03 PM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote:

> In this case, it's useful to differentiate between (i) the AMI that Galaxy
> Cloud uses and (ii) the Galaxy code running on the cloud. I suspect that
> (ii) is out of data for you; this is not (yet) automatically updated, even
> when starting a new instance.
>
> Try using the admin console to update to the most recent Galaxy dist using
> this URL:
>
> https://bitbucket.org/galaxy/galaxy-dist/
>
> (not galaxy-central, as is the default)
>
> Best,
> J.
>
> On Oct 31, 2012, at 8:36 PM, Mohammad Heydarian wrote:
>
> We are running "galaxy-cloudman-2011-03-22 (ami-da58aab3)".
>
> Our latest instance was loaded up just last week.
>
> Thanks!
>
> Cheers,
> Mo Heydarian
>
> PhD candidate
> The Johns Hopkins School of Medicine
> Department of Biological Chemistry
> 725 Wolfe Street
> 414 Hunterian
> Baltimore, MD 21205
>
>
>
> On Wed, Oct 31, 2012 at 8:30 PM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote:
>
>> Given that this doesn't seem to be happening on our public server or on
>> local instances, my best guess is that the issue is old code. Are you
>> running the most recent dist?
>>
>> J.
>>
>>
>> On Oct 31, 2012, at 7:37 PM, Mohammad Heydarian wrote:
>>
>> We are still getting empty TopHat output files on our Galaxy instance on
>> the cloud. We see that TopHat is generating data while the tool is running
>> (by monitoring our disk usage on the Amazon cloud), but the output is
>> "empty" files.
>>
>> Is anyone else having this issue? Does anyone have any suggestions?
>>
>> Many thanks in advance!
>>
>>
>> Cheers,
>> Mo Heydarian
>>
>>
>>
>> On Mon, Oct 15, 2012 at 4:53 AM, Joachim Jacob <joachim.ja...@vib.be>wrote:
>>
>>> The same here.
>>>
>>> Cheers,
>>> Joachim
>>>
>>> --
>>> Joachim Jacob, PhD
>>>
>>> Rijvisschestraat 120, 9052 Zwijnaarde
>>> Tel: +32 9 244.66.34
>>> Bioinformatics Training and Services (BITS)
>>> http://www.bits.vib.be
>>> @bitsatvib
>>>
>>>
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>>>
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>
>
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