Question: Condor And Galaxy
0
gravatar for gorkemerdogan35
4.1 years ago by
Turkey
gorkemerdogan3510 wrote:

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"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
<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 • 1.5k views
ADD COMMENTlink modified 4.1 years ago by Martin Čech ♦♦ 4.8k • written 4.1 years ago by gorkemerdogan3510
2

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 REPLYlink written 4.1 years ago by jmchilton1.1k
3
gravatar for Bjoern Gruening
4.1 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

it seems that you are missing the handlers section.

<handlers><handler id="main"/></handlers>

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

Cheers,

Bjoern

ADD COMMENTlink written 4.1 years ago by Bjoern Gruening5.1k
0
gravatar for gorkemerdogan35
4.1 years ago by
Turkey
gorkemerdogan3510 wrote:

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

ADD COMMENTlink written 4.1 years ago by gorkemerdogan3510
0
gravatar for gorkemerdogan35
4.1 years ago by
Turkey
gorkemerdogan3510 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 COMMENTlink written 4.1 years ago by gorkemerdogan3510

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

ADD REPLYlink written 4.1 years ago by Bjoern Gruening5.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 112 users visited in the last hour