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" 
<n...@bx.psu.edu<mailto:n...@bx.psu.edu>> wrote:

On Aug 18, 2014, at 9:55 AM, Iry Witham 
<iry.wit...@jax.org<mailto:iry.wit...@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" 
<jmchil...@gmail.com<mailto:jmchil...@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.wit...@jax.org<mailto: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<mailto: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<mailto: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<mailto:mma...@benaroyaresearch.org>>
Date: Thursday, August 14, 2014 12:48 PM
To: Iry Witham <iry.wit...@jax.org<mailto:iry.wit...@jax.org>>, 
"galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>"
<galaxy-dev@lists.bx.psu.edu<mailto: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<mailto:iry.wit...@jax.org>>
Date: Thursday, August 14, 2014 9:34 AM
To: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto: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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