Note that cgi run from the command-line will use $HOME/.hg.conf which must be configured appropriately. You will probably want to use the settings in your cgi-bin/hg.conf for the most part.
-Galt On 10/06/10 04:07, Maximilian Haussler wrote: > 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] <mailto:[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] > <mailto:[email protected]>> > > To: [email protected] <mailto:[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] <mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
