Hello Sai, If you file is very large, this could cause the Custom track loader to stall. The alternative is to use bigBed format. A description of the data format and how to convert bed -> bigBed is in this link:
http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format Ftp location to obtain pre-compiled utilities (such as bedToBigBed): http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ ftp hgdownload.cse.ucsc.edu user name: anonymous password: your email address CT Help: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks If you file is small and you would like help to make sure the browser/track lines are formatted OK, please send these lines, any options set on the Custom track page, and a few lines of your BED data pasted into an email, back to the list, and we can aid with troubleshooting. Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/8/10 3:11 PM, Saigopal Thota wrote: > Hi, > > I have successfully setup the genome browser with your help but I am facing > problem adding custom tracks. I tried uploading a file, pasting data into > the text area, and pasting URL of data file into the text area. In all the > three cases, the page doesnot move to a different one and it stays in the > same page while the loading wheel of the browser tab keeps moving as if it > is loading something. Did someone report a similar problem before or do you > have any idea what am I missing in making it work. The kind of file I am > trying to upload is in proper BED format. > > Thanks, > Sai > > On Wed, Apr 7, 2010 at 12:28 PM, Saigopal Thota<[email protected]> wrote: > >> Hi all, >> >> Thanks for your time in replying to my question. I have found one other way >> to let apache server see the files without extension as cgi files. I created >> a .htaccess file in the cgi-bin folder of genome browser and put DefaultType >> application/x-httpd-cgi into it. I think if anyone has a similar problem, >> they can try this too. >> >> Once again thanks in providing your ideas. >> >> - >> saigopal >> >> On Wed, Apr 7, 2010 at 8:51 AM, Maximilian Haussler<[email protected] >>> wrote: >> >>> Saigopal probably has already figured this out. I've stumbled over the >>> same problem before. >>> >>> The usual tip in apache docs to use AddHandler does not work as the cgis >>> not not end in CGI. The browser does this differently that todays standards >>> and ScriptAlias is sometimes not explained in apache help pages. >>> >>> The cgis need to be in the scriptAlias directory. I've added this to the >>> wiki. >>> >>> Max >>> >>> On Thu, Apr 1, 2010 at 7:50 PM, Hiram Clawson<[email protected]> wrote: >>> >>>> This depends upon where you place these CGI binaries. They are probably >>>> only going to work correctly if you place them in the apache cgi-bin/ >>>> directory. Are you trying to locate them elsewhere ? >>>> >>>> --Hiram >>>> >>>> Saigopal Thota wrote: >>>>> Hi, >>>>> >>>>> I am a student at UC Davis. We are trying to setup genome browser for >>>> the >>>>> data we have and I successfully created the minimal browser >>>> installation. >>>>> But the problem I am facing is that the CGI files (hgGateway etc.) are >>>>> present without .cgi extensions. Our Apache server is not recognizing >>>> them >>>>> as cgi files and not executing them correctly. As a result I see >>>> garbage >>>>> data on the browser. Can you please help me to enable the setting in >>>> apache >>>>> to execute any file as cgi, since the UCSC genome browser works without >>>> any >>>>> extension, you may have some idea of how that can be done. Thanks for >>>> your >>>>> time in advance. >>>>> >>>>> Sai >>>> _______________________________________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>> >>> >>> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
