Condor And Galaxy

Question: Condor And Galaxy

4.4 years ago by

Turkey

Hello , I get an error in job_conf.xml. İ use galaxy jobs with htcondor and edit job_conf.xml file but getting an error.

Error:

`galaxy.jobs DEBUG 2014-06-25 15:07:23,001 Loading job configuration from ./job_conf.xml
Traceback (most recent call last):
File "/home/bionia/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/bionia/galaxy-dist/lib/galaxy/app.py", line 77, in __init__
self.job_config = jobs.JobConfiguration(self)
File "/home/bionia/galaxy-dist/lib/galaxy/jobs/__init__.py", line 107, in __init__
self.__parse_job_conf_xml(tree)
File "/home/bionia/galaxy-dist/lib/galaxy/jobs/__init__.py", line 161, in __parse_job_conf_xml
self.default_handler_id = self.__get_default(handlers, self.handlers.keys())
File "/home/bionia/galaxy-dist/lib/galaxy/jobs/__init__.py", line 304, in __get_default
rval = parent.get('default')
AttributeError: 'NoneType' object has no attribute 'get'`

job_conf.xml file:

`<?xml version="1.0"?>

<job_conf>
<plugins>
<plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner"/>
</plugins>
<destinations>
<destination id="condor" runner="condor"/>
</destinations>
</job_conf>`

job conf htcondor newbie • 1.6k views

ADD COMMENT • link •

modified 4.4 years ago by Martin Čech ♦♦ 4.9k • written 4.4 years ago by gorkemerdogan35 • 10

Thanks Bjoern for the fix. I seem to make this mistake a lot myself - I have created a Trello card to make the error message more clear to just make the handler section optional (https://trello.com/c/6bJiqPTS).

ADD REPLY • link written 4.4 years ago by jmchilton ♦ 1.1k

4.4 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

it seems that you are missing the handlers section.

Can you start from the fresh job_conf.xml.sample_basic file?

Cheers,

Bjoern

ADD COMMENT • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k

4.4 years ago by

gorkemerdogan35 • 10

Turkey

gorkemerdogan35 • 10 wrote:

I didn't see this mistake. Now it's okay. Thank you so much

ADD COMMENT • link written 4.4 years ago by gorkemerdogan35 • 10

4.4 years ago by

gorkemerdogan35 • 10

Turkey

gorkemerdogan35 • 10 wrote:

I am giving some error again.But now running job and directiroy nonexistent.This error is :

/var/lib/condor/execute/dir_2647/condor_exec.exe: 15: /var/lib/condor/execute/dir_2647/condor_exec.exe: cannot create /home/bionia/clusterfs/galaxy/galaxy-dist/database/job_working_directory/000/2/__instrument_core_galaxy_slots: Directory nonexistent
/var/lib/condor/execute/dir_2647/condor_exec.exe: 16: /var/lib/condor/execute/dir_2647/condor_exec.exe: cannot create /home/bionia/clusterfs/galaxy/galaxy-dist/database/job_working_directory/000/2/__instrument_core_epoch_start: Directory nonexistent
/var/lib/condor/execute/dir_2647/condor_exec.exe: 17: cd: can't cd to /home/bionia/clusterfs/galaxy/galaxy-dist/database/job_working_directory/000/2
Traceback (most recent call last):
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/tools/data_source/upload.py", line 10, in <module>
    import galaxy.model
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 9, in <module>
    eggs.require("pexpect")
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 404, in require
    c = Crate( None )
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 260, in __init__
    self.parse()
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 265, in parse
    self.parse_egg_section( self.config.items( 'eggs:platform' ), self.config.items( 'tags' ), True )
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 275, in parse_egg_section
    egg = egg_class( name=name, version=version, tag=tag, url=url, platform=platform, crate=self )
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 50, in __init__
    self.set_distribution()
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 60, in set_distribution
    self.set_dir()
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 54, in set_dir
    os.makedirs( self.dir )
  File "/usr/lib/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/home/bionia/clusterfs/galaxy/galaxy-dist/eggs'
Traceback (most recent call last):
  File "./scripts/set_metadata.py", line 31, in <module>
    import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 9, in <module>
    eggs.require("pexpect")
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 404, in require
    c = Crate( None )
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 260, in __init__
    self.parse()
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 265, in parse
    self.parse_egg_section( self.config.items( 'eggs:platform' ), self.config.items( 'tags' ), True )
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 275, in parse_egg_section
    egg = egg_class( name=name, version=version, tag=tag, url=url, platform=platform, crate=self )
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 50, in __init__
    self.set_distribution()
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 60, in set_distribution
    self.set_dir()
  File "/home/bionia/clusterfs/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 54, in set_dir
    os.makedirs( self.dir )
  File "/usr/lib/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/home/bionia/clusterfs/galaxy/galaxy-dist/eggs'
/var/lib/condor/execute/dir_2647/condor_exec.exe: 19: /var/lib/condor/execute/dir_2647/condor_exec.exe: cannot create /home/bionia/clusterfs/galaxy/galaxy-dist/database/pbs/galaxy_2.ec: Directory nonexistent
/var/lib/condor/execute/dir_2647/condor_exec.exe: 20: /var/lib/condor/execute/dir_2647/condor_exec.exe: cannot create /home/bionia/clusterfs/galaxy/galaxy-dist/database/job_working_directory/000/2/__instrument_core_epoch_end: Directory nonexistent

ADD COMMENT • link written 4.4 years ago by gorkemerdogan35 • 10

As stated in the error message, it seems you have some permission problems to access the galaxy-dist folder on your cluster nodes.

ADD REPLY • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k

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