Intensity tracks must be in the bigwig (.bw) format. Previously, those were created for us by Chee-Hong at JGI from BAM files.

genomebrowser.shore.mbari.org is hosted on nextgen.shore.mbari.org. The username is geneadm, for the password see Sebastian Sudek, Mike McCann, Brian Schlining, or Rich Schramm.

Copy the bigwig file to nextgen with

scp /path/to/bigwig geneadm@nextgen.shore.mbari.org:/data/genome_browser_data/bigwigs
password:<fill in password>

Login to nextgen

ssh geneadm@nextgen.shore.mbari.org
password:<fill in password>

Add the new track to the database (CCMP1545_v3 or RCC299_v3)

hgBbiDbLink CCMP1545_v3 <your_trackname> /data/genome_browser_data/bigwigs/<new_bigwig.bg>

Tell the browser about the new track

formatTrack
(then follow prompts)

And restart the browser

cd /data/genome_browser_data/genomes/trackDb && ./loadTracks.sh

Your new tracks should now show up under the blue RNASeq bar in the browser. They are hidden by default.

Tip for pros: you can access the mysql database as -ubrowser -pgenome. This might be useful if you want to remove tracks.

To remove tracks from the browser page, edit the pages under

/data/genome_browser_data/genomes/trackDb/CCMP1545/CCMP1545_v3/trackDb.ra
and
/data/genome_browser_data/genomes/trackDb/RCC299/RCC299_v3/trackDb.ra