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
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