Hi Nate,

We were able to get upgraded to pbs-python 4.4.0 after having to modify some c++ code that was causing errors with the _py.so.  We now have it running, but I am trying to get the references to work for the tools I have installed from the tool shed.  They can't seem to find the correct path.  

Thanks,
Iry

Sent from my iPhone

On Aug 18, 2014, at 5:08 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:

On Aug 18, 2014, at 9:55 AM, Iry Witham <Iry.Witham@jax.org> wrote:

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

Hi Iry,

It looks like we need to upgrade to pbs_python 4.4.0: https://oss.trac.surfsara.nl/pbs_python/ticket/34

The pbs_python 4.4.0 source is on our eggs server - could you update the version to 4.4.0 in /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs.ini and re-scramble the egg and let us know if this fixes it?

Thanks,
--nate



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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and other Galaxy lists, please use the interface at:
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The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.