I have not seen this before - are you able to submit things as your
Galaxy user from the command line? Are their logs on the PBS side that
give any more clues?

-John

On Fri, Aug 15, 2014 at 2:01 PM, Iry Witham <iry.wit...@jax.org> wrote:
> Hi John,
>
>         It looks like it may be related to PBS and Torque.  I am currently
> running torque-4.2.5.  I scrambled the pbs-python eggs and it is now
> running pbs-python 4.3.5.  The good thing is I am now getting an attempt
> to submit to pbs, but all jobs are failing.  This is the error:
>
> galaxy.jobs.handler DEBUG 2014-08-15 13:10:37,822 (16) Dispatching to pbs
> runner
> galaxy.jobs DEBUG 2014-08-15 13:10:41,110 (16) Persisting job destination
> (destination id: pbs:////-l nodes=1:ppn=1,walltime=20:00:00)
> galaxy.jobs.handler INFO 2014-08-15 13:10:41,145 (16) Job dispatched
> galaxy.tools.deps DEBUG 2014-08-15 13:10:42,338 Building dependency shell
> command for dependency 'samtools'
> galaxy.tools.deps WARNING 2014-08-15 13:10:42,339 Failed to resolve
> dependency on 'samtools', ignoring
> galaxy.jobs.runners.pbs ERROR 2014-08-15 13:11:33,507 Connection to PBS
> server for submit failed: 15007: No permission
>
>
> Iry
>
> On 8/15/14 12:11 PM, "John Chilton" <jmchil...@gmail.com> wrote:
>
>>Okay - I just checked out a clean Galaxy without modifications and I
>>don't see any problems with uploads. So this is likely something to do
>>with your setup - if I had to guess I would guess that your
>>job_conf.xml configuration is somehow incorrect - the job is getting
>>creating but nothing is running it. Can you verify this by looking in
>>the logs? I would imagine you do see lines like:
>>
>>galaxy.tools.actions.upload_common INFO 2014-08-15 12:04:04,306 tool
>>upload1 created job id 2
>>
>>for the uploads but nothing like:
>>
>>galaxy.jobs.runners DEBUG 2014-08-15 12:04:05,119 (2) command is:
>>python
>>/home/john/workspace/galaxy-central-fresh/tools/data_source/upload.py
>>....
>>
>>You could also verify this is the problem by doing something other
>>than uploading - maybe a data source tool? I have attached a tool that
>>doesn't require any existing files or external data sources that I use
>>for testing stuff like this - maybe see if it runs?
>>
>>If no jobs run - can you attach your job_conf.xml and we can try to
>>debug the problem from there.
>>
>>If other tools run than it is likely not a job related problem - in
>>that case can you answer some questions - Are you using a proxy - if
>>so which one? Can you attach the configuration? Is the upload.xml tool
>>in your tool_conf.xml? Have you made modifications to it?
>>
>>-John
>>
>>On Fri, Aug 15, 2014 at 10:47 AM, Iry Witham <iry.wit...@jax.org> wrote:
>>> I have checked and everything appears correct.  I did notice that in the
>>> /database/tmp/upload_store/ there are files that when I cat them they
>>>are
>>> the files I am/have attempted to upload.  However, they do not get
>>>moved to
>>> the /ftp directory.  I am wondering if this is due to a
>>>misconfiguration in
>>> the universe.wsgi.ini or if it could be related to proftpd or postgres.
>>> Unfortunately I am under a very tight deadline and need to figure this
>>>out.
>>> Any assistance will be appreciated.
>>>
>>> Thanks,
>>> Iry
>>>
>>> From: Michael Mason <mma...@benaroyaresearch.org>
>>> Date: Thursday, August 14, 2014 12:48 PM
>>> To: Iry Witham <iry.wit...@jax.org>, "galaxy-dev@lists.bx.psu.edu"
>>> <galaxy-dev@lists.bx.psu.edu>
>>> Subject: Re: [galaxy-dev] Upload file not working with new install
>>>
>>> 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.wit...@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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