c4473ca7e4dd9383e7b03b8e306b1f57aa071ae3 mspeir Wed Feb 11 08:38:40 2026 -0800 minor chnages to wording based on CR, refs #37095 diff --git docs/hubs/contributedTracks.md docs/hubs/contributedTracks.md index 6bdc93da683..379ea961a37 100644 --- docs/hubs/contributedTracks.md +++ docs/hubs/contributedTracks.md @@ -1,125 +1,125 @@ --- title: "Contributed Tracks" --- 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. -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. +This page outlines the procedures for submitting a set of tracks to the +UCSC Genome Browser for inclusion in the default view of a genome assembly. +This procedure is for developers that have a number of tracks +to submit to a single genome assembly, or a set of tracks to deliver to multiple +genome assemblies. Development process: - Develop your annotations in a track hub under your control. - Provide a reference to your development track hub to the genome browser for inclusion consideration. - By following the suggested outline, the browser will be able to efficiently add your annotations to the genome browser system. ## Your track hub file/directory structure ``` +-- 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 ``` ## Requirements Assembly names need to be the NCBI GenBank accession names to identify the corresponding assembly. **GCF\_...** or **GCA\_...** All annotations must have appropriate documentation. The track hub directory structure must be as described here. ## Example hub.txt file ``` 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:: +# 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 ``` The **genomes.txt** file specifies the target assemblies. The **descriptionUrl** link refers to **documentation.html** for this track hub. Since the data is uniform for all the tracks, a single **documentation.html** can be sufficient for all documentation. ## Example genomes.txt file ``` 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 ``` List each assembly for which you have calculated annotations. The **trackDb.txt** file defines the tracks. To emphasize again, the assembly names must be the GenBank accession identifier, e.g.: **'GCF\_016077325.2'**. Refer to the [full list](https://hgdownload.gi.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt) of all GenArk repository assemblies to find the correct identifier for your genome. ## Example trackDb.txt file ``` 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 ``` Since all the annotations are the same type, a single **trackDb.txt** file is sufficient for all assemblies. The **html** link refers to **../documentation.html** as used in the **hub.txt** file. For documentation structure, you can follow the typical UCSC track description format with sections for: **Description**, **Methods**, **Credits**, **References**. We provide an [example template](/goldenPath/help/examples/hubExamples/templatePage.html), or see, for example, the description page of a [typical UCSC track](/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=recombRate2).