Hi,

I was trying to use the boxplot tool (Graph/Display Data) from within
our local Galaxy instance (just updated yesterday). I faced a couple
of issues while trying to generate boxplots. I was wondering which
gnuplot version is actually recommended?

While working with gnuplot version "4.0 patchlevel 0", one of the
error messages was:

line 0: undefined variable: tmargin

gnuplot> plot '/tools/galaxy/database/files/000/dataset_94.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(
'/tools/galaxy/database/files/000/dataset_94.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

this can be overcome this by deleting "tmargin" form the "boxplot.xml" file.

The second error message:

gnuplot> plot '/tools/galaxy/database/files/000/dataset_94.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(
'/tools/galaxy/database/files/000/dataset_94.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

Again, I just removed "whiskerbars" and I got my plot...

After getting updated my gnuplot (version 4.4), those issues were
solved but there was another one related to the fonts, message:

"Could not find/open font when opening font "arial", using internal
non-scalable font"

This could also be "fixed" by setting explicitly the font in the
boxplot.xml  (according to what I was just told, arial is proprietary
and in some linux systems could represent an issue...):

For instance:

set term png size ${graph_size} font
"/usr/share/fonts/liberation/LiberationSans-Regular.ttf,12"

anyway, is there any gnuplot version recommended? Could the
boxplot.xml be fixed/adapted to cope with those issues?

cheers,
Erick
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