374e1f49a6756a875e4603394686cbb707cd746b mspeir Sun Feb 8 16:59:04 2026 -0800 minor tweaks to formatting and wording of some sections, refs #37043 diff --git docs/hubs/contributedTracks.md docs/hubs/contributedTracks.md index da5776b2fee..5fc8b71ee9f 100644 --- docs/hubs/contributedTracks.md +++ docs/hubs/contributedTracks.md @@ -1,123 +1,126 @@ --- 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. Development process: -1. Develop your annotations in a track hub under your control. -2. Provide a reference to your development track hub to the genome browser +- 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. -3. By following the suggested outline, the browser will be able to +- 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:: # 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 or the UCSC database name, e.g.: **'GCF\_016077325.2', or 'hg38', 'mm39'**. -You can find a full list of all GenArk repository assemblies at: -[assembly hub list](https://hgdownload.gi.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt) +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 +For documentation structure, you can follow the typical UCSC track description format with sections for: **Description**, **Methods**, **Credits**, -**References**. For example: -[typical UCSC track](/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=recombRate2) documentation. +**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).