6d5744572234650664785eab8d4a443bc0908506 mspeir Wed Feb 18 09:34:00 2026 -0800 adding link to hubBasics and email address, refs #37043 diff --git docs/hubs/contributedTracks.md docs/hubs/contributedTracks.md index 6e212fcd7d9..81f32f4ab16 100644 --- docs/hubs/contributedTracks.md +++ docs/hubs/contributedTracks.md @@ -1,127 +1,130 @@ --- 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 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. +- Develop your annotations in a track hub under your control. Follow the steps on + our [track hub basics](hubBasics.html) page to create your hub. - 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. +- [Contact us](mailto:genome-www@soe.ucsc.edu) when you're ready to submit your + tracks for consideration. ## 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 A hub must meet the following requirements before being accepted for consideration: - Assembly names must be NCBI GenBank accession names (i.e. GCF\_\* or GCA\_\*) to identify the corresponding assembly. - All annotations must have appropriate documentation as described below. - The track hub directory structure must match that described on this page. ## 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: # 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).