[Genome] binary program phyloGif

[Galt Barber]

we still build linux redhat 32-bit cgis:

rsync -a rsync://hgdownload.cse.ucsc.edu/cgi-bin-i386/phyloGif .

Good news! I have tested this and it will run from the commandline
without needing the cart and mysql, and it will make the gif
from the nh tree file.  If you run it as a cgi from apache, however,
it will expect the cart and database to be as in our
environment here.

Command-line Usage Examples:
   phyloGif -phyloGif_tree=tree.nh [options] > phylo.gif
   phyloGif -phyloGif_tree='(A:0.1,B:0.1)' [options] > phylo.gif

also

   echo "(A:0.1,B:0.1)" | phyloGif -phyloGif_tree=stdin > test.gif

good luck!

-Galt


On Thu, 7 Jun 2007, Yufeng Zhai wrote:

> Dear Galt,
>
> This is the only command line program I can found on the web to
> convert tree files to image, and I don't have and don't need mysql
> database. We need this program to convert a number of dynamically
> generated trees, could you please tell me how can I get a compiled
> copy of this program?
>
> Thank you very much
>
> Yufeng
>
> On Jun 6, 2007, at 11:09 AM, Galt Barber wrote:
>
> >
> > The big problem is that this cgi
> > uses the "cart" library to store user settings
> > and that creates a dependency on the entire
> > system which means a mysql db to store the
> > cart and so on.
> >
> > However, you can simply hit our system with a
> > url and make your gif output.
> >
> > Here's an example:
> >
> > http://hgwdev.cse.ucsc.edu/cgi-bin/phyloGif?
> > phyloGif_width=200&phyloGif_height=120&phyloGif_branchLengths=1&phyloG
> > if_tree=((A:0.1,B:0.1):0.2,C:0.15);
> >
> > Note that you can put in any tree and set options and submit.
> > Then look at the URL that is in your browser.
> > Cut and paste the URL to wherever you want to use it.
> > You could even make a script or program that submits
> > these URLs and gets the .gif output back.
> >
> > Let us know if you have more questions.
> >
> > -Galt
> >
> >
> > On Tue, 5 Jun 2007, Yufeng Zhai wrote:
> >
> >> Dear Sir or Madam
> >>
> >> How are you doing.
> >>
> >> I am trying to get a copy of binary phyloGif for my redhat linux
> >> machine. Because I can't compile the whole program package
> >> successfully, it always gave me error message that related to mysql
> >> library . I am not an administrator and I just need this single
> >> program. Could you please send me a copy of it? my system is redhat
> >> linux on a P4 computer?
> >>
> >> Thank you very much.
> >>
> >> Sincerely
> >>
> >> Yufeng
> >>
> >> _______________________________________________
> >> Genome maillist  -  Genome at soe.ucsc.edu
> >> http://www.soe.ucsc.edu/mailman/listinfo/genome
> >>
> >
>