Hi Sai, Did you already see the custom track documentation here?: http://genomewiki.ucsc.edu/index.php/Using_custom_track_database
(This is the same information that is in the kent/src/product/README.customTracks.dataBase file.) For future reference, it is better to send mirror-related questions to our mirror mailing list: [email protected]. You can also browse and search old mirror-related questions starting from this page: http://genome.ucsc.edu/contacts.html#mirror . -- Brooke Rhead UCSC Genome Bioinformatics Group On 04/09/10 11:57, Saigopal Thota wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
