bigDataUrl is only for these types: bigWig, bigBed, bam, vcfData These are binary formats that usually incorporate compression internally for further savings and in some cases have been optimized for efficient random access and may have views at multiple zoom levels.
All other custom track types are just text. If it sees a line beginning with a URL beginning with ftp:// http:// https:// then it will read that URL inserting its contents inline. This works just like an #include <file> in C and other languages. It is recursive, i.e. if the text contains another line starting with a url it will include those lines too and so on. If the url extension has .gz .zip .bz2 it will automatically decompress the incoming lines of text. Note that the protocol file:// is not supported and wouldn't work anyway. A trackline must be present for each track. For bigDatUrl type tracks, one line defines the entire track. For other text types, the track line may either precede a URL that is to be included, or because of how it works, there may be a track line in the included file itself. Whenever the system sees an expanded text line starting with "track " it knows that a new custom track definition is beginning. For all recursive included url lines (not bigDataUrl), the resulting text is just as if all lines were expanded into memory and then processed. Because of this, you can create higherarchies of urls. You can create a set by making a text file that just includes the several tracks' urls or data. Then you can create another text file that includes the urls of the sets you made. Providing the url to that file will cause the system to recursively load an entire tree of custom tracks. The contents of the custom track are passed as you know in hgct_customText, and must be url-encoded. Because both the browser and our library can only handle a url that is of limited length (around 1500 bytes), you would not want to try to create massive input data passed directly in the hgct_customText. Instead, put your text into a file and pass its url to hgct_customText. -Galt 6/9/2011 7:39 AM, Rebecca Hudson: > Our lab is trying to streamline the process of creating links that can be > clicked directly rather than loaded in the Custom Track tool. (Links of the > form: > http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr21:33038447-33041505&hgct_customText=track%20type=bigBed%20name=myBigBedTrack%20description=%22a%20bigBed%20track%22%20visibility=full%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb) > > We've had success creating links for viewing bigWig tracks; but most > of our files are in .wig.gz format. > > When we attempt to visit this link (names removed): > http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr8:128451376-128834335&hgct_customText=track%20type=wiggle_0%20name=%22trackName%22%20description=%22trackName%201,25%22%20color=233,43,75%20visibility=full%20horizGrid=on%20yLineOnOff=off%20autoScale=on%20alwaysZero=on%20graphType=points%20maxHeightPixels=22:33:44%20windowingFunction=mean+whiskers%20smoothingWindow=off%20priority=12%20viewLimits=0:50%20bigDataUrl=https://ourdomain.edu/wiggleData.wig.gz > > > This error is displayed at the top of the window. > * track load error (track name='ct_trackName_5944'): > ERROR: wigEncode: empty input file: 'stdin' > > We've had success loading the same file manually as a custom track; it's not > empty. > > Is it possible to load a wig.gz file as a custom track using the bigDataUrl? > What could we be missing? > > thanks! > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
