Hi, Thanks for your quick replies. We are setting up our own mirror of the genome browser on our server. I was able to upload the scaffold fasta file into the database without a problem. Now, to that I want to add custom tracks (which we have in .bed, .gff3, .bam, msam formats). But they gave errors like trash directory not accessible and customTrash database not found. Then I have created them and gave necessary permissions. After doing all this, I am not getting any errors, but the page does not load into the next one. As you mentioned, the files are big and so I copied the first 10 lines from the bed file and pasted them in the text area to upload. But the same problem is repeated. I am pasting the data I tried to upload as custom track below. If you find any anamoly in the format, please let me know. Also is there a pre-determined set of steps to be done (other than the trash directory and customTrash db) for custom tracks to work? If so, please guide me through those steps. Again thanks for your wonderful support.
Thanks, Sai ------------------------------------------------------------------------------------------------------------------------------------------------------------------- bed file lines I tried:: track name=junctions description="TopHat junctions" scaffold03123 36371 36938 JUNC00000001 20 - 36371 36938 255,0,0 2 63,70 0,497 scaffold03123 38731 38961 JUNC00000002 1 - 38731 38961 255,0,0 2 9,66 0,164 scaffold03123 56351 56571 JUNC00000003 30 - 56351 56571 255,0,0 2 67,65 0,155 scaffold03123 56593 57432 JUNC00000004 1 - 56593 57432 255,0,0 2 20,55 0,784 scaffold03123 56569 57447 JUNC00000005 5 - 56569 57447 255,0,0 2 47,70 0,808 scaffold03123 57495 59950 JUNC00000006 17 - 57495 59950 255,0,0 2 66,64 0,2391 scaffold03123 59996 63418 JUNC00000007 15 - 59996 63418 255,0,0 2 63,70 0,3352 scaffold03123 60084 63406 JUNC00000008 1 - 60084 63406 255,0,0 2 17,58 0,3264 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- On Thu, Apr 8, 2010 at 7:26 PM, Jennifer Jackson <[email protected]> wrote: > 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
