In addition to the direct command-line method, you can use wget, curl, perl or python with web libraries, etc.
Here is an example from one of our mailing list users of driving hgGenome via URL: http://hg/cgi-bin/hgGenome?db=hg18&hgGenome_dataSetName=hmYRI_CEU_tdt_TDTgg&hgGenome_dataSetDescription=GalaxyGG_data&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess&hgGenome_columnLabels=first%20row&hgGenome_maxVal=&hgGenome_labelVals=&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http%3A%2F%2Fgalaxy%2Fdisplay_as%3Fid%3D351%26display_app%3Ducsc&hgGenome_doSubmitUpload=submit In particular, note that the data is made available to hgGenome via URL. That URL is then itself url-encoded inside the larger URL. &hgGenome_uploadFile=url-encoded-url-to-actual-data-in-genome-graphs-text-input -format You could also use an html form POST and provide the data contents directly via hgGenome_uploadFile form variable. The output will be a graphic file (png) stored in trash. You will have to parse the output to find the url or path. When run from the commandline, cgis will make directories and files under both . and ../trash -Galt On 10/05/10 15:53, Alex Reynolds 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
