Adding New Tracks to a browser installation

Adding a custom track

Gotchas

Your .bed file better not have any browser or track lines if you want the loader to work

You need to hop all over the source tree like a frog on a griddle to get things done...

A BED track description for a custom SNP track

The .bed file has lines like this:

chr22   49512530        49512531        rs8137951       0       +       49512530        49512531        255,0,0
chr22   49518559        49518560        rs756638        0       +       49518559        49518560        255,0,0
chr22   49522492        49522493        rs3810648       0       +       49522492        49522493        255,0,0
chr22   49524956        49524957        rs2285395       0       +       49524956        49524957        255,0,0
chrX    100017093       100017094       rs5921682       0       +       100017093       100017094       255,0,0
chrX    100019802       100019803       rs5967204       0       -       100019802       100019803       255,0,0

Load the .bed file into a custom track called Ill550v3 Note the .bed file must have NO browser or track lines - otehrwise hgLoadBed will barf

/var/www/cgi-bin/loader/hgLoadBed -noBin  -tab hg18 Ill550v3 /home/rerla/public_html/illHH550v3.BED

Adjust your trackDb.ra file

I'm working (eg) on meme in

/home/rerla/hg18/kent/src/hg/makeDb/trackDb/human/hg18

I add these settings - they seem to work the way I want, allowing the name field from the .bed file to appear in full view:

track Ill550v3
priority 20.1   
shortLabel Illum550kv3           
longLabel Illumina 550k v3 snps
visibility pack
type bed 9 .          
color 255,0,0   
group varRep                 
thickDrawItem on

Recompile the trackDB

make alpha DBS=hg18