The Galaxy history (https://usegalaxy.org/u/aloraine/h/cold-stress-fastq) listed in the release testing instructions (https://wiki.transvar.org/display/ITD/Galaxy) does not include a wig or bigwig file.

See if Ann would also needs those.

Yes, we need all three. Send them to Ann when they are ready.

We have each of those file types in the human genome, see smoke testing quickload:
http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/

The Galaxy test set is all in Arabidopsis, but ... does it have to be all in one genome?
--upside to making A. thaliana files: we have multiple complete test sets.
--downside of making A. thaliana files: takes effort, not sure exactly how much.

BigBed:
Use bedToBigBed from blat suite, see https://genome.ucsc.edu/goldenpath/help/bigBed.html

BigWig:
Use wigToBigWig from blat suite, see https://genome.ucsc.edu/goldenpath/help/bigWig.html

Wig:
Use bigWigToWig from blat suite, see help page.

Need to pick out some bed file to use for the initial input....

The files are in a google drive folder which I have shared with Ann.

I attached the file of instructions to make the three file formats. Requires the blat suite.

I ran into some difficulty with making a bigbed file from the TAIR10.bed file. The bedToBigBed converter complained about something in the description field(s). After I removed those fields, the converter made a bigbed file, but IGB would not display the data (just loaded empty space). I created issue IGBF-1272 to address this. Rather than convert all of the chromosome names, I picked a different started file that used names to match the A. thaliana genome: Pollen.bed. The bedToBigBed converter complained about scores that were greater than 1000, so I added a step to set all scores to 0. With this, IGB will load the file and display features. But each feature is shown as a single block (original file was junctions--each feature is two blocks), and the strand info seems to have been lost. I created issue IGBF-1273 to investigate this.

I am reassigning to Ann to add these files to the Galaxy history for testing.

uploaded to public Galaxy History "Open Galaxy files in Integrated Genome Browser"

For two of the files, the file genome ("database") is set to "Arabidopsis_thaliana_TAIR10", and they appear in IGB in the Arabidopsis genome.

The wig file is set to "arabidopsis", so it appears in IGB in a custom genome, apart from any other data.

I am reassigning to Ann to correct the genome attribute of the wig file.

All files now have Galaxy genome version set to "Arabidopsis thaliana TAIR10"

The wig files shows up in the right genome now.
All files appear as they do when I load them from my local machine.

I am marking this issue as complete.