Haden, Kirt wrote:
> Hi,
> 
> 
> 
> When I run Galaxy under Python 2.7, I am unable to run SAM to BAM tools 
> without getting the following error (below). The same configuration with 
> Python 2.6 does not have an issue. The error seems to indicate bx_python eggs 
> are not fetchable. What am I doing wrong?

Hey Kirt,

Are you running it on a machine with no Internet access?  If not, can
you run:

    python ./scripts/fetch_eggs.py

With python set to your 2.7 version?

Thanks,
--nate

> 
> 
> 
> Error report below:
> 
> 
> 
> GALAXY TOOL ERROR REPORT
> 
> ------------------------
> 
> 
> 
> This error report was sent from the Galaxy instance hosted on the server 
> "ussd-dev-lnx01.illumina.com"
> 
> -----------------------------------------------------------------------------
> 
> This is in reference to dataset id 301 from history id 68
> 
> -----------------------------------------------------------------------------
> 
> You should be able to view the history containing the related history item
> 
> 
> 
> 7: SAM-to-BAM on data 6: converted BAM
> 
> 
> 
> by logging in as a Galaxy admin user to the Galaxy instance referenced above 
> and pointing your browser to the following link.
> 
> 
> 
> ussd-dev-lnx01.illumina.com/history/view?id=42e99d98e0ee2844
> 
> -----------------------------------------------------------------------------
> 
> The user 'kha...@illumina.com' provided the following information:
> 
> 
> 
> 
> 
> -----------------------------------------------------------------------------
> 
> job id: 200
> 
> tool id: sam_to_bam
> 
> -----------------------------------------------------------------------------
> 
> job command line:
> 
> python /home/galaxy/eval/sept09/galaxy-central/tools/samtools/sam_to_bam.py   
>     
> --input1=/home/galaxy/production/Sept06/galaxy-central/database/files/000/dataset_300.dat
>          --dbkey=PhiX        
> --output1=/home/galaxy/production/Sept06/galaxy-central/database/files/000/dataset_301.dat
>        --index_dir=/home/galaxy/eval/sept09/galaxy-central/tool-data
> 
> -----------------------------------------------------------------------------
> 
> job stderr:
> 
> Traceback (most recent call last):
> 
>   File 
> "/home/galaxy/eval/sept09/galaxy-central/tools/samtools/sam_to_bam.py", line 
> 14, in ?
> 
>     import pkg_resources; pkg_resources.require( "bx-python" )
> 
>   File "/home/galaxy/eval/sept09/galaxy-central/lib/galaxy/eggs/__init__.py", 
> line 415, in require
> 
>    raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
> 
> galaxy.eggs.EggNotFetchable: ['bx_python']
> 
> 
> 
> -----------------------------------------------------------------------------
> 
> job stdout:
> 
> 
> 
> -----------------------------------------------------------------------------
> 
> job info:
> 
> None
> 
> -----------------------------------------------------------------------------
> 
> job traceback:
> 
> None
> 
> -----------------------------------------------------------------------------
> 
> (This is an automated message).
> 
> 
> Thanks,
> 
> Kirt Haden
> Sr. Mgr. Engineering
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858.202.4655
> Fax: 858.202.4545
> Email: kha...@illumina.com<mailto:kha...@illumina.com>
> Website: www.illumina.com<http://www.illumina.com/>
> 

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