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" <jmchilton@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.Witham@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 <MMason@benaroyaresearch.org> Date: Thursday, August 14, 2014 12:48 PM To: Iry Witham <iry.witham@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.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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