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Question: ImportError when running job on local cluster
1
gravatar for danielfortin86
2.8 years ago by
danielfortin86 • 110
United States
danielfortin86 • 110 wrote:

Hi,

I just got my galaxy installation to use an SGE cluster. The jobs seem to run successfully, however I get this error related to metadata (see below). Is this a bug or some problem with my configuration? 

Job Error Message:

​Traceback (most recent call last):
  File "/remote/data/users/galaxyd/job_working_directory/000/65/set_metadata_FtbTIv.py", line 1, in <module>
    from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
ImportError: No module named galaxy_ext.metadata.set_metadata

Thanks!

 
metadata cluster importerror • 1.0k views
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modified 2.8 years ago • written 2.8 years ago by danielfortin86 • 110

Associated: see related prior post: Problem with SGE_ROOT, SGE / drmaa with Galaxy (updated)

ADD REPLY • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
2
gravatar for danielfortin86
2.8 years ago by
danielfortin86 • 110
United States
danielfortin86 • 110 wrote:

Hi, 

 

I discovered the fix in this commit:

https://github.com/galaxyproject/galaxy/pull/289/files

I needed to specify the "embed_metadata_in_job" parameter so that the metadata refresh is done locally

    <destination id="SGE" runner="sge">
                <param id="embed_metadata_in_job">False</param>
                <param id="nativeSpecification">-q all.q</param>
        </destination>

 
ADD COMMENT • link written 2.8 years ago by danielfortin86 • 110
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