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).
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).
-- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. <golharam.vcf>_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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).
-- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. <golharam.vcf>_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Ryan Golhar wrote:
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?
At present, no. We plan to implement some sort of dependency management in the (hopefully near) future.
--nate
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).
-- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. <golharam.vcf>_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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