e49a713e18b15cfc70cf4248102ddd5c9170db95
mspeir
  Sun Feb 8 16:46:09 2026 -0800
adding Hiram's new page about contributing tracks to GenArk genomes, refs #37043

diff --git docs/hubs/contributedTracks.md docs/hubs/contributedTracks.md
new file mode 100644
index 00000000000..da5776b2fee
--- /dev/null
+++ docs/hubs/contributedTracks.md
@@ -0,0 +1,123 @@
+---
+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
+   for inclusion consideration.
+3. 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)
+
+## 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
+format with sections for: **Description**, **Methods**, **Credits**,
+**References**. For example:
+[typical UCSC track](/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=recombRate2) documentation.