Here are some examples that illustrate Hiram's excellent response: You can put one or more tracks into a simple text page that you put on your webserver. e.g. page url: http://myserver.edu/coolCustomTrackSet1 which contains the following text:
track name=track1 type=bigwig bigDataUrl=http://myserver.edu/coolTrack1.bw track name=track2 type=bigwig bigDataUrl=http://myserver.edu/coolTrack2.bw track name=track3 type=bigwig bigDataUrl=http://myserver.edu/coolTrack3.bw You can even group them hierarchically if you want by providing a higher-level includer text file: e.g. page url: http://myserver.edu/coolSuperSetX which contains the following text: http://myserver.edu/coolCustomTrackSet1 http://myserver.edu/coolCustomTrackSet2 So to share the entire super set with your user, he just needs to paste in http://myserver.edu/coolSuperSetX to the custom track form. You can even make a page where the user clicks on a link that will go and post that superset url to the hgCustom or hgTracks cgi. Here is an example link: http://hgwdev.cse.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr11:116199665-116209156&hgt.customText=http://myserver.edu/coolSuperSetX (note that the email programs might split the track line, but it's just one line.) -Galt On 05/18/11 12:25, Hiram Clawson wrote: > You can construct custom track files with your own procedures and provide > a URL in the genome browser that will use those custom tracks in > a browser view. > > 1. construct your BAM and bigWig/bigBed files and place them on a WEB server > so > they can be accessed via a URL reference > http://genome.ucsc.edu/goldenPath/help/bam.html > http://genome.ucsc.edu/goldenPath/help/bigWig.html > http://genome.ucsc.edu/goldenPath/help/bigBed.html > 2. construct a small text file consisting of the 'track' definition lines for > each > BAM/bigWig/bigBed file where the bigDataUrl refers to the files you > constructed > in step 1. Place this small file also on your WEB server so it can be > accessed > via a URL. > http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK > 3. publish a URL to the genome browser hgTracks CGI, including the > db=<ucscDatabaseName> > and hgt.customText=<url to your file from step 2> > http://genome.ucsc.edu/goldenPath/help/customTrack.html#ADD_CT > http://genome.ucsc.edu/goldenPath/help/customTrack.html > > Your data consumer users only need to know about the URL you publish in step > 3. > > Access that genome browser URL and the custom tracks will be in that view. > You can also update the data in those tracks merely by refreshing the > contents of your BAM/bigWig/bigBed files at their same URL. You do not > need to change anything else. The system will automatically use the > updated files when next viewed. > > --Hiram > > Elia Stupka wrote: >> Hello there, >> >> we use quite heavily the viewing of BAM and BIGWIG files located on our web >> servers to create sessions for UCL scientists, and although the greatest >> part of our pipeline for NGS analysis is automated we always end up adding >> custom tracks and saving sessions manually, is there a way to do the process >> automatically, through some form of API? >> >> thank you and best regards, >> >> Elia Stupka >> >> >> --- >> Scientific Director - Bioinformatics, UCL Genomics >> Senior Lecturer, Bioinformatics >> >> UCL Cancer Institute >> Paul O' Gorman Building >> University College London >> 72, Huntley Street >> WC1E 6BT >> London >> UK >> >> Institute of Cell and Molecular Science >> Barts and The London School of Medicine and Dentistry >> 4 Newark Street >> Whitechapel >> London >> E1 2AT >> >> Office (UCL): +44 207 679 6493 >> Fax: +44 0207 6796817 >> Office (ICMS): +44 0207 8822374 >> >> Mobile: +44 787 6478912 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
