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?
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
Website:
www.illumina.com