Hi Alex, If you have your own mirror, you can run all CGI programs from the command line (see: http://genomewiki.ucsc.edu/index.php/Browser_Installation#If_it_doesn.27t_work... ):
* Use the arguments from the URL and replace the & with spaces * Call the CGI from a command line and copy the arguments just after the CGI, like this "/var/www/cgi-bin/hgc hgsid=337 o=14394787 t=14395353 It should create the images which you can then use in your own cgi scripts. If you need more details no this, don't hesitate to email the list again. cheers Max On Tue, Oct 5, 2010 at 11:53 PM, Alex Reynolds <[email protected]>wrote: > I understand that. Our lab has a local installation of a UCSC Genome > Browser, so I would have access to those database resources. > > Is there a way to issue (for example) a "wget" or "curl" command, packaging > the requisite POST and GET variables in an HTTP request to hgGenome, so as > to automate figure generation? > > -Alex > > On Oct 5, 2010, at 3:43 PM, Galt Barber wrote: > > > > > The cgi programs are typically intended to be run inside of apache > > and they use additional resources such as databases and the cart > > and various binary data formats. > > > > -Galt > > > > ----- Original Message ----- > > From: "Alex Reynolds" <[email protected]> > > To: [email protected] > > Sent: Tuesday, October 5, 2010 1:18:40 PM GMT -08:00 US/Canada Pacific > > Subject: [Genome] Automating hgGenome > > > > I am making genome-wide figures using the Genome Graphs tool of the UCSC > browser. This looks and works great. > > > > However, as I have a number of these to make, I'd like to try to automate > the process. > > > > I downloaded the hgGenome cgi-bin binary via instructions at > http://genome.ucsc.edu/admin/jk-install.html, but I'm not sure what > arguments it takes, or if I can use it as a command-line tool to automate > making figures. > > > > Is anyone familiar with hgGenome or its use on the command line? > > > > Thanks, > > Alex > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
