Add color for bed track

[lalalagartija]

Hi,
I am trying to add colors to a bigbed track without sucess.
I tried
jbrowse add-track file.bigbed -a genome --load copy --out /var/www/html/jbrowse2/ --config '{"displays": [{"displayId": "basicdisplay","type":"LinearBasicDisplay", "renderer": {"color1": "green", "type": "SvgFeatureRenderer"}}]}'
and
jbrowse add-track file.bigbed -a genome --load copy --out /var/www/html/jbrowse2/ --config '{"displays": [{"renderer": {"color1": "green"}}]}'

none of them worked
Thank you,

[garrettjstevens]

Hi @lalalagartija,

I tried using the same --config as your first example, and it worked for me, so I'm not sure what's going on. Could you provide some more information about what you see? For example, a screenshot of your track and/or a copy of the track config that gets added to your "config.json".

For reference, this is what I see when running that command (modified to use my own bigbed file):

[lalalagartija]

Hi,
Thank you for your answer.
Actually I deleted the old files because I want to get different colors for each gene. I tried a new method that is still unsucessfull..
./bedToBigBed -as=blast_clusters.as2 -type=bed9+2 -extraIndex=nothing,Cluster blast_clusters.bed9 chrom.sizes myBigBed2.bb
browse add-track myBigBed.bb -a Virus1 --load copy --out /var/www/html/viruses/ --force

The resulting track on Jbrowse2 is empty. I can't see any of the bed features.
I used a .as file that looks like this :
"
table name
"UCSC Genes for Pithovirus_massiliensis with color plus"
(
string chrom; "Reference sequence chromosome or scaffold"
uint chromStart; "Start position of feature on chromosome"
uint chromEnd; "End position of feature on chromosome"
string name; "Name of gene"
uint score; "Score"
char[1] strand; "+ or - for strand"
uint thickStart; "Coding region start"
uint thickEnd; "Coding region end"
uint reserved; "Green on + strand, Red on - strand"
string nothing; "Gene Symbol"
string Cluster; "SWISS-PROT protein Accession number"
)
"
bed file :
"
Virus1 22888 23064 name1 0 + 22888 23064 60,18,208 . Cluster1
Virus1 121877 122058 name2 0 + 121877 122058 60,18,208 . Cluster1
Virus1 181522 181702 name3 0 + 181522 181702 60,18,208 . Cluster1
Virus1 199225 199406 name4 0 + 199225 199406 60,18,208 . Cluster1
Virus1 199575 199755 name5 0 + 199575 199755 60,18,208 . Cluster1
Virus1 199856 200035 name6 0 - 199856 200035 60,18,208 . Cluster1
Virus1 238392 238573 name7 0 + 238392 238573 60,18,208 . Cluster1
Virus1 286233 286409 name8 0 - 286233 286409 60,18,208 . Cluster1
Virus1 545032 545210 name9 0 - 545032 545210 60,18,208 . Cluster1
Virus1 620602 620784 name10 0 + 620602 620784 60,18,208 . Cluster1

"
And the config.json for this track is :
"
{
"type": "FeatureTrack",
"trackId": "myBigBed",
"name": "myBigBed",
"adapter": {
"type": "BigBedAdapter",
"bigBedLocation": {
"uri": "myBigBed.bb",
"locationType": "UriLocation"
}
},
"assemblyNames": [
"Virus1"
]
}
"

Do you happen to know what I am doing wrong ,
Thank you very much

[lalalagartija]

Hi !
I solved my issue. There was womething wrong with my bed file then I regenerated it and I added rgb() to the color column.
The command line I did was :
jbrowse add-track blast_clusters_simple.bb -a Virus1 --load copy --out /var/www/html/viruses/ --force --config '{"displays": [{"displayId": "basicdisplay","type":"LinearBasicDisplay", "renderer": {"color1": "jexl:get(feature, @thecolor@)", "type": "SvgFeatureRenderer"}}]}'

then
sed -i "s/@thecolor@/'thecolor'/g" /var/www/html/viruses/config.json