Yes, this seem to be the issue. The Python on the compute nodes is not 
configured correctly. Thanks.

Kirt


-----Original Message-----
From: Nate Coraor [mailto:n...@bx.psu.edu] 
Sent: Friday, September 30, 2011 10:04 AM
To: Chorny, Ilya
Cc: Daniel Blankenberg; Haden, Kirt; 'galaxy-dev@lists.bx.psu.edu'
Subject: Re: [galaxy-dev] Python2.7 SAM to BAM Egg Not Fetchable

If this is running on a cluster, is there any chance the version of Python used 
on your cluster nodes was compiled with UCS-2 Unicode?  You can check by 
running scripts/get_platforms.py on the host in question using the desired 
python binary.

The eggs you have only work with UCS-4 Unicode.

--nate

Chorny, Ilya wrote:
> Same permissions as the 2.6 egg. 
> 
> 
> 
> -----Original Message-----
> From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
> Sent: Friday, September 30, 2011 8:59 AM
> To: Chorny, Ilya
> Cc: Nate Coraor; Haden, Kirt; 'galaxy-dev@lists.bx.psu.edu'
> Subject: Re: [galaxy-dev] Python2.7 SAM to BAM Egg Not Fetchable
> 
> Is this instance using the run job as user patch, and if so, does the user 
> running the job have permission to access the egg?
> 
> 
> 
> Thanks for using Galaxy,
> 
> Dan
> 
> 
> On Sep 30, 2011, at 11:36 AM, Chorny, Ilya wrote:
> 
> > The egg is there, but the error still shows up.
> > 
> > -----Original Message-----
> > From: galaxy-dev-boun...@lists.bx.psu.edu
> > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate 
> > Coraor
> > Sent: Friday, September 30, 2011 6:40 AM
> > To: Haden, Kirt
> > Cc: 'galaxy-dev@lists.bx.psu.edu'
> > Subject: Re: [galaxy-dev] Python2.7 SAM to BAM Egg Not Fetchable
> > 
> > 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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> >> 
> >>  http://lists.bx.psu.edu/
> > 
> > ___________________________________________________________
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> > 
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> > 
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> > 
> >  http://lists.bx.psu.edu/
> 
> 

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