Re: [Dart-help] help with windowlicker

[Ian H. <ih...@be...>]

Hi Marcin,

first, sorry I didn't reply to your earlier email to me, been a bit busy
here. There is actually a dart-help mailing list...

http://biowiki.org/DartMailingLists

...but it'll pretty much end up in the same inboxes if you email
holmes-lab instead ;)


second, the error you're getting means that xrate couldn't be run. If
you just type "xrate -h" from your command prompt, do you get a help
message? Or do you have to type in the entire path to xrate, e.g.
"/nfs/src/dart/bin/xrate -h" or whatever?

If the latter, then it's likely that windowlicker just can't find the
xrate binary. You can test this by typing "windowlicker.pl -h" and
looking at the "-x" option, whose default value is the path that
windowlicker is trying to use.

Best fix for this is to set the DARTDIR environment variable to the root
of your DART installation (/nfs/src/dart in the above example). You can
also use windowlicker's -x option to tell it the path to the xrate
executable.


third, if the above doesn't fix your problem, can you email me the
actual file you're having problems with (if it's huge, then gzip or bzip
it first) so I can try to reproduce the issue.


Hope this helps!
Ian



PS I am still trying to get around to reading your guide tree
manuscript. It will happen though!


marcin joachimiak wrote:
> hello,
> 
> I have the DART package built and running at the syntax help level.
> Formatting the FASTA file to Stockholm was successful.
> I've tried running windowlicker on the stocholm data and got:
> 
> -bash-3.00$ perl /usr2/people/gtl/bin/dart/perl/windowlicker.pl
> DvH_DP4_G20_mVISTA.stock
> xrate failed (check command-line options? they were: xrate )
> 
> So I assume there are more required arguments? And how would I supply
> the reference grammars?
> 
> thanks,
> marcin