Hi Matthew and Guru,
Thanks for the info and the fix! I'll just update my Galaxy setup to
get the required changes...
Cheers,
Pi
On 3•Aug•2009, at 10:43 PM, Guruprasad Ananda wrote:
Hello,
The suggested changes have been made to the bar chart tool, and are
available in the changeset 2522:789741370e80.
Thanks for using Galaxy,
Guru
Galaxy team.
On Aug 3, 2009, at 8:55 AM, Matthew Eldridge wrote:
> Hi Pieter,
>
> Perhaps you already had a response about this, but if not I also
> get a similar error with gnuplot trying to open an X11 display. I
> fixed this by adding the following line to tools/plotting/
> bar_chart.py right at the bottom of the file just before the call
> to main:
>
> Gnuplot.gp.GnuplotOpts.default_term = 'png'
>
> The other thing I noticed about the bar chart tool is that it seems
> to be configured in bar_chart.xml to output a PDF file when in fact
> it produces a PNG image so I had to fix that also.
>
> Kind regards
> Matt
>
> 2009/7/29 Pieter Neerincx <pieter.neerincx(a)gmail.com>
> Hi,
>
> The bar chart generator does not work for me. It looks like gnuplot
> is complaining (see below or attached screenshot), but I'm not sure
> if this is the problem. I'm on CentOS 5.3 and have gnuplot version
> 4.0.0-14.el5. In addition I installed gnuplot-py 1.8. How do I fix
> this?
>
> Cheers,
>
> Pi
>
> gnuplot> set style histogram clustered gap 5 title offset character
> 0, 0, 0 ^ line 0: expecting 'data', 'function', 'line',
'fill' or
> 'arrow' line 0: undefined variable: in line 0: undefined variable:
> invert
> gnuplot> set style data histograms ^ line 0: expecting 'lines',
> 'points', 'linespoints', 'dots', 'impulses',
'yerrorbars',
> 'xerrorbars', 'xyerrorbars', 'steps', 'fsteps',
'histeps',
> 'filledcurves', 'boxes', 'boxerrorbars',
'boxxyerrorbars',
> 'vectors', 'financebars', 'candlesticks',
'errorlines',
> 'xerrorlines', 'yerrorlines', 'xyerrorlines', 'pm3d'
> gnuplot: unable to open display 'localhost:13.0'
> gnuplot: X11 aborted.
>
>
>
> -------------------------------------------------------------
> Biomolecular Mass Spectrometry and Proteomics
> Utrecht University
>
> Visiting address:
> H.R. Kruyt building room O607
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
>
> Mail address:
> P.O. box 80.082
> 3508 TB Utrecht
> The Netherlands
>
> phone: +31 (0)6-143 66 783
> email: pieter.neerincx(a)gmail.com
> skype: pieter.online
> ------------------------------------------------------------
>
>
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Guruprasad Ananda
Graduate Student
Bioinformatics and Genomics
The Pennsylvania State University
-------------------------------------------------------------
Biomolecular Mass Spectrometry and Proteomics
Utrecht University
Visiting address:
H.R. Kruyt building room O607
Padualaan 8
3584 CH Utrecht
The Netherlands
Mail address:
P.O. box 80.082
3508 TB Utrecht
The Netherlands
phone: +31 (0)6-143 66 783
email: pieter.neerincx(a)gmail.com
skype: pieter.online
------------------------------------------------------------