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@gmail.com skype: pieter.online ------------------------------------------------------------
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@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@gmail.com skype: pieter.online ------------------------------------------------------------
_______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
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@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@gmail.com skype: pieter.online ------------------------------------------------------------
_______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University
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@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@gmail.com skype: pieter.online ------------------------------------------------------------
_______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
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@gmail.com skype: pieter.online ------------------------------------------------------------
participants (3)
-
Guruprasad Ananda -
Matthew Eldridge -
Pieter Neerincx