Trackster visualizations: no additional datasets can be added to existing

[jennaj]

The exact same problems at ORG & EU. Didn't test on a local.

Problem: Trackster will not allow additional datasets to be added to an existing visualization after opened, even when those inputs have the same dbkey (genome) assigned. Can get a bit further but still no loading by click into previously created/saved Trackster vis from an individual dataset and try to add it in... but the "Add to visualization" button does nothing. "Cancel" will back you out, so that part is working.

Clue? Are the fasta/len indexes not really being accessed?? Could show up in GUI as not finding data with "add datasets" or actually loaded into a saved "vis" plus prevent genome navigation functions from displaying. The chromosome pull-down is missing at the top. No way to change the chromosome or set a region. One can "drag" into a sub-region, then are stuck there or can go smaller again. No indication of what chromosome is being viewed, or region, unless guess from chromosome tick labels or by zooming in on a feature and comparing it to the input data lines.

Ticket: Found in late 10/19 under release19.09, and this ticket from @dannon is related but we are not sure if it will solve the entire problem (yet): galaxyproject/galaxy#7224

Related or Not?

1. No way to create a visualization unless there is some dataset available to launch it from. One used to be able to create an empty visualization with NO datasets at all (create viz backbone, add datasets after in batch or serially). How to reproduce: 1) create an empty history 2) go to Visualize > Create Visualization 3) get a red warning "There is no suitable dataset in your current history which can be visualized with this plugin." So, no simple "Create New Vis" by picking the dbkey & optionally renaming from default vis name.
2. Opening a visualization, doing nothing, then closing gives a warning that "unsaved changes will be lost". There are no changes. Saving or not saving, the same viz cannot have data loaded directly when open or added in from another dataset. Is there some metadata difference while active versus not? For comparison, Workflows only give this warning when closing if something was actually changed.

Test histories: Include data for one full hg19 gtf and the rest hg19 only chr1 for datatypes gtf, bam, sam, and selection of beds: bed3, bed4, bed6, bed12.

• https://usegalaxy.org/u/jen/h/test-trackster
• https://usegalaxy.eu/u/jenj/h/test-trackster

Test visualizations: No other datasets show up under "add datasets" from the history OR in data libraries. Defaults or with filters applied.

Created from the hg19 chr1 bam dataset (data 3): No data shows up (?) or I couldn't find it. Can't tell which chromosome is displayed -- trackster chrom ticks do not match up with chr1 (what's in the data) or chr10 (first chrom in coord-sorted index).

• https://usegalaxy.org/u/jen/v/test-trackster-hg19-chr1-bam
• https://usegalaxy.eu/u/jenj/v/test-trackster-hg19-chr1-bam

Created from the hg19 full gtf dataset (data 10): Data shows up. Appears to be from chr1 (?) -- GTF coordinates versus Trackster for individual items match up. Original chrom ticks still wrong for chr1 or chr10. Looks like the data is truncated length-wise (horizontal, max around 250m bases).

• https://usegalaxy.org/u/jen/v/test-trackster-hg19-full-gtf
• https://usegalaxy.eu/u/jenj/v/test-trackster-hg19-full-gtf

Reported by users at both usegalaxy.org and usegalaxy.eu.

Work-around for end-users: Use alternative genome browsers. If the database is assigned to your data (built-in index or custom build), visualization options will appear as links in the expanded datasets. May include UCSC main, IGV, and others.

Screenshots, from EU but ORG exactly the same...

test-trackster-no-genome-navigation-drag-in-get-stuck (chr1 hg19 bam created). No data?

test-trackster-no-genome-navigation-drag-in-get-stuck2 (full hg19 gtf created). Has data, matches up with input: chr1 unknown exon 2115899 2116952 . - . gene_id "C1orf86"; transcript_id "NM_001146310"; gene_name "C1orf86"; p_id "P10611"; tss_id "TSS5339";

test-trackster-cannot-load-from-dataset-into-saved-vis

test-trackster-cannot-create-empty-vis

test-trackster-cannot-load-data-from-library

test-trackster-cannot-load-data-from-history