451babbb2d02e1d3803422f96a054f96ad5ad78c hiram Wed Jan 28 14:28:04 2026 -0800 initial ontent to describe contributed track procedure refs #34706 diff --git src/hg/htdocs/contribTracks.html src/hg/htdocs/contribTracks.html new file mode 100755 index 00000000000..b39ce964bca --- /dev/null +++ src/hg/htdocs/contribTracks.html @@ -0,0 +1,139 @@ +<!DOCTYPE html> +<!--#set var="TITLE" value="Genome Browser Contributed Tracks" --> +<!--#set var="ROOT" value="." --> + +<!-- Relative paths to support mirror sites with non-standard GB docs install --> +<!--#include virtual="$ROOT/inc/gbPageStart.html" --> + +<h1>Contributed Tracks</h1> + +<p> +Researchers are creating annotations for hundreds of assemblies +in one process, or creating a number of annotations for one assembly. +It would be useful to the wider research community to have these +annotations included in the default browser view on those assemblies. +</p> + +<p> +This discussion outlines procedures for submitting a set of tracks to the +browser for inclusion in the default view of a genome assembly. + This procedure is for developers of tracks that have a number of tracks +to submit to one assembly, or a set of tracks to deliver to a multiple +set of genome assemblies. +</p> + +<p> +Development process: +<ul> +<li>Develop your annotations in a track hub under your control.</li> +<li>Provide a reference to your development track hub to the genome browser + for inclusion consideration.</li> +<li>By following the suggested outline, the browser will be able to + efficiently add your annotations to the genome browser system.</li> +</ul> +</p> + +<h2>Your track hub file/directory structure</h2> +<pre> ++-- hub.txt ++-- genomes.txt ++-- documentation.html ++-- GCA_000260495.2/ +| +-- trackDb.txt +| +-- veupathGenes.bb +| +-- veupathGenes.gtf.gz ++-- GCF_014441545.1/ +| +-- trackDb.txt +| +-- veupathGenes.gtf.gz +| +-- veupathGenes.bb ++-- GCF_014108235.1/ +| +-- trackDb.txt +| +-- veupathGenes.gtf.gz +| +-- veupathGenes.bb +</pre> + +<h2>Requirements</h2> +<p> +Assembly names need to be the NCBI GenBank accession names to +identify the corresponding assembly. <b>GCF_...</b> or <b>GCA_...</b> +</p> +<p>All annotations must have appropriate documentation.</p> +<p>The track hub directory structure must be as described here.</p> + +<h2>Example <b>hub.txt</b> file</h2> + +<pre> +hub PAG_2026_GenArk_Contrib_Example +shortLabel PAG 2026 GenArk tracks +longLabel PAG 2026 example of contributed tracks to UCSC GenArk assemblies +email genome@soe.ucsc.edu +genomesFile genomes.txt +descriptionUrl documentation.html + +# comments: +# load this hub with a reference to this hub.txt file: +# https://genome-test.gi.ucsc.edu/~hiram/BRC/contrib/hub.txt + +# for example, to show this track hub in the genome browser:: + +# https://genome.ucsc.edu/cgi-bin/hgTracks?genome=GCA_000260495.2& +# hubUrl=https://genome-test.gi.ucsc.edu/~hiram/BRC/contrib/hub.txt +</pre> +<p> +The <b>genomes.txt</b> file specifies the target assemblies. +The <b>descriptionUrl</b> link refers to <b>documentation.html</b> for +this track hub. Since the data is uniform for all the tracks, +a single <b>documentation.html</b> can be sufficient for all documentation. +</p> + +<h2>Example <b>genomes.txt</b> file</h2> +<pre> +genome GCA_000260495.2 +trackDb GCA_000260495.2/trackDb.txt + +genome GCF_014441545.1 +trackDb GCF_014441545.1/trackDb.txt + +genome GCF_014108235.1 +trackDb GCF_014108235.1/trackDb.txt +</pre> +<p> +List each assembly for which you have calculated annotations. +The <b>trackDb.txt</b> file defines the tracks. To emphasize again, +the assembly names must be the GenBank accession identifier or +the UCSC database name, e.g.: <b>'GCF_016077325.2', or 'hg38', 'mm39'</b>. +You can find a full list of all GenArk repository assemblies at: +<a href='https://hgdownload.gi.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt' +target=_blank>assembly hub list</a> +</p> + +<h2>Example <b>trackDb.txt</b> file</h2> +<pre> +track VEuPathDBGeneModels +shortLabel PAG 2026 contrib +longLabel PAG 2026 - demonstrating contributed tracks to UCSC GenArk assemblies +group genes +type bigBed 12 . +visibility pack +labelFields name +searchIndex name +bigDataUrl veupathGenes.bb +colorByStrand 0,0,122 157,60,32 +dataVersion VEuPathDB release 68 +html ../documentation + +# can be multiple track definitions here for other annotations +</pre> +<p> +Since all the annotations are the same type, a single <b>trackDb.txt</b> +file is sufficient for all assemblies. The <b>html</b> link refers +to <b>../documenation.html</b> as used in the <b>hub.txt</b> file. +For documentation structure, you can follow the typical UCSC track +format with sections for: <b>Description</b>, <b>Methods</b>, <b>Credits</b>, +<b>References</b>. For example: +<a href='/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=recombRate2' +target=_blank>typical UCSC track</a> documentation. +</p> + + +<!--#include virtual="$ROOT/inc/gbPageEnd.html" -->