No joy. I cannot even find acknowledgement that galaxy is loading any of
my tools or of those in the directory that follows. The tool is called
analyze_reads and "cat paster.log| grep analyze_r| less produces an end of
file. The last tool load showing is vcf_tools_extract, but all beyond that
also load and are usable in workflows EXCEPT analyze_reads when any
parameter is specified type="float" or type="integer". The tools I am
using to edit the files are set for UTF-8 encoding but are not in fact
capable of sending anything but plain old ASCII. (the very basic vi as my
X isn't working at the moment).
Still examining paster.log was an education. I am pleased that it got by
many reported errors and still picked up my scan_reads tool.
I guess my next act is to run siege and see if all the instances are
Thank you much for the suggestion. I really needed to see paster.log.
On Mon, Apr 9, 2012 at 3:28 PM, Ross <ross.laza...@gmail.com> wrote:
> First thing I'd do would be to check paster.log after trying to load
> your new tool and I'll bet there's an 8 bit character or something in
> your text somewhere that causes the tool parser to barf - the error in
> paster.log will tell you the line and character where loading stopped?
> On Mon, Apr 9, 2012 at 6:24 PM, Michael Moore
> <michaelglennmo...@gmail.com> wrote:
> > I am testing galaxy for wide use, and I have legacy text files that call
> > algorithms, sorts, and displays. One such has a tool.xml file with 10
> > parameters, one select, three integer, and one float, with the rest text
> > the moment. (some will be type="data" later if the runs equate to the
> > we do outside galaxy)
> > The tool does not show up. Firefox, emacs and vim all agree that it is
> > well-formed, and galaxy has been properly bounced. I experimented with
> > removing parameters and found with 7 parameters, I did not have the
> > then I noticed that all of them had been changed to text or select in my
> > desperation to make it show up for placement on the workflow. I
> returned to
> > 10 parameters, but this time all type="select" and type="text", and
> > everything worked. But slipping even one integer, even with the
> > min max and default tags, and the tool would disappear on restart.
> > Am I looking at a bug, or is there something I need to be doing to make
> > tool visible with numeric parameters?
> > MGM
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
> > in your mail client. To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> > http://lists.bx.psu.edu/
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: