Hi John, I was able to work through this since it was related to pbs on the cluster. However, I am still having issues. This is the error I am getting: galaxy.tools.genome_index DEBUG 2014-08-18 09:31:56,819 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2014-08-18 09:31:56,825 Starting job handler galaxy.jobs INFO 2014-08-18 09:31:56,825 Handler 'handler1' will load all configured runner plugins galaxy.jobs.runners DEBUG 2014-08-18 09:31:56,829 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2014-08-18 09:31:57,073 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners DEBUG 2014-08-18 09:31:57,104 Starting 3 LWRRunner workers galaxy.jobs.runners.lwr_client.manager INFO 2014-08-18 09:31:57,197 Setting LWR client class to standard, non-caching variant. galaxy.jobs DEBUG 2014-08-18 09:31:57,228 Loaded job runner 'galaxy.jobs.runners.lwr:LwrJobRunner' as 'lwr' Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/webapps/galaxy/bu ildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line 144, in __init__ self.job_manager = manager.JobManager( self ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/manager.py", line 23, in __init__ self.job_handler = handler.JobHandler( app ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py", line 31, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py", line 583, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/__init__.py" , line 496, in get_job_runner_plugins module = __import__( module_name ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/runners/pbs. py", line 32, in <module> raise Exception( egg_message % str( e ) ) Exception: The 'pbs' runner depends on 'pbs_python' which is not installed or not configured properly. Galaxy's "scramble" system should make this installation simple, please follow the instructions found at: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster Additional errors may follow: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pbs_python-4.3.5-py2.6-l inux-x86_64-ucs4.egg/_pbs.so: undefined symbol: log_record Removing PID file handler1.pid I am running the following: galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> qsub --about HomeDir: /var/spool/torque InstallDir: /usr/local Server: rockhopper BuildDir: /root/torque-4.2.5 BuildUser: root BuildHost: galaxy2 BuildDate: Sat Aug 16 11:17:00 EDT 2014 Version: 4.2.5 Commit: 39f78e588b3a47a6c7bed1004ec7b5d0ccf24288 The handler.pid are being removed. Thanks, Iry On 8/18/14 9:16 AM, "John Chilton" <jmchilton@gmail.com> wrote:
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.Witham@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" <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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