I'm running Version 4.0 patchlevel 0. I'll upgrade it. Is there a way to scan through the list of pre-reqs and make sure all the version match? Thanks, Ryan Daniel Blankenberg wrote:
What version of gnuplot are you using? gnuplot 4.2 patchlevel 2 or greater is required.
Thanks for using Galaxy,
Dan
On May 4, 2010, at 9:56 AM, Ryan Golhar wrote:
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" ----------------------------------------------------------------------------- This is in reference to dataset id 50 from history id 2 ----------------------------------------------------------------------------- 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 ----------------------------------------------------------------------------- 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
----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).
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