+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: +
++-- 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 ++ +
+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.
+ ++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. +
+ ++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 +
+ ++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 ../documenation.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 documentation. +
+ + +