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:nate@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:dan@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 'khaden@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: khaden@illumina.com<mailto:khaden@illumina.com> Website: www.illumina.com<http://www.illumina.com/>
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