New subject: [Fwd: Galaxy tool error report from golharam@umdnj.edu]

4 May 2010


      Hi all - I'm trying to plot the data from a fastq file uploaded to my 
local instance.  When I rung the boxplot app on the uploaded file, I get 
this error.  It has something to do with the parameters to plot in 
gnuplot not being right.  I don't know gnuplot well enough (at all 
actually) so I don't know what is wrong.
The error show is in reference to 'tmargin', but actually I think it has 
something to do with the whiskerbars parameter.  How do I know this? 
When I run:
gnuplot> plot 
'/mnt/ibmfcarray/galaxydata/database/files/000/dataset_46.dat' using 
1:7:11:12:9 with candlesticks lt 1  lw 1 title 'Quartiles'
I see a plot, but when I add
gnuplot> plot 
'/mnt/ibmfcarray/galaxydata/database/files/000/dataset_46.dat' using 
1:7:11:12:9 with candlesticks lt 1  lw 1 title 'Quartiles' whiskerbars,
I get the same error.
GALAXY TOOL ERROR REPORT
------------------------
This error report was sent from the Galaxy instance hosted on the server
"genomes.umdnj.edu"
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This is in reference to dataset id 50 from history id 2
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You should be able to view the history containing the related history item
14: Boxplot on data 10
by logging in as a Galaxy admin user to the Galaxy instance referenced above
and pointing your browser to the following link.
genomes.umdnj.edu/history/view?id=529fd61ab1c6cc36
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The user 'golharam@umdnj.edu' provided the following information:
-----------------------------------------------------------------------------
job id: 12
tool id: qual_stats_boxplot
-----------------------------------------------------------------------------
job command line:
gnuplot < '/opt/galaxy_dist/database/job_working_directory/12/tmpnKQZFP' 
2>&1 || echo "Error running gnuplot." >&2
-----------------------------------------------------------------------------
job stderr:
Error running gnuplot.
-----------------------------------------------------------------------------
job stdout:
          line 0: undefined variable: tmargin
gnuplot> plot 
'/mnt/ibmfcarray/galaxydata/database/files/000/dataset_46.dat' using 
1:7:11:12:9 with candlesticks lt 1  lw 1 title 'Quartiles' whiskerbars, 
       ''         using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 
'Medians',      "< python -c "for xval, yvals in [ ( fields[1 - 1], 
fields[13 - 1].split( ',' ) ) for fields in [ line.rstrip( '\n\r' 
).split( '\t' ) for line in open( 
'/mnt/ibmfcarray/galaxydata/database/files/000/dataset_46.dat' ) if not 
line.startswith( '#' ) ] if len( fields ) > max( 1 - 1, 13 - 1 ) ]: 
print '\n'.join( [ '%s\t%s' % ( xval, yval ) for yval in yvals if yval 
] )"" using 1:2 with points pt 29 title 'Outliers'
^
          line 0: ';' expected
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job info:
None
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job traceback:
None
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(This is an automated message).
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