Hello Sebastien,
Thank you very much for your question about loading local tracks on
your mirror. Is there a particular reason you want local MySQL tables
and not hubs or bigBed/bigWig/BAM file tracks? It may be easier to
just use track hubs so you don't have to mess with loading and
maintaining a separate trackDb table.
Either way, I followed your steps and was able to successfully create
a local track:
# follow the steps but don't do the full mm10 mirror
$ sudo bash browserSetup.sh -b install
$ sudo bash browserSetup.sh -t main mirror mm10
$ sudo bash browserSetup.sh addTools
$ printf "db.user=browser\ndb.password=genome\ndb.host=127.0.0.1" >
~/.hg.conf; chmod 600 ~/.hg.conf
$ sudo vim /usr/local/apache/cgi-bin/hg.conf # manually configure
hg.conf with defaultGenome=Mouse and db.trackDb=trackDb_local,trackDb
$ mkdir src && cd src
$ wget
https://raw.githubusercontent.com/ucscGenomeBrowser/kent/1b09e68a8fca8098b818be0586055c53549db384/src/hg/lib/trackDb.sql
$ wget
https://raw.githubusercontent.com/ucscGenomeBrowser/kent/1b09e68a8fca8098b818be0586055c53549db384/src/hg/lib/hgFindSpec.sql
$ cd ..
$ mkdir -p tracks/mm10
$ printf "include trackDb.RNAseq.ra" >> ~/tracks/mm10/trackDb.ra
$ touch ~/tracks/mm10/hgFindSpec_local.tab
$ sqlDir="${HOME}/src"
$ DB=mm10
# make a one line bed file "chr1 1 10000"
$ vim mm10.bed
$ cat mm10.bed
chr1 1 10000
# load it and make sure it's there
$ hgLoadBed mm10 simpleTrack mm10.bed
$ hgsql -e "show tables mm10"
# make a simple ra file, which I assume you've already done?
$ vim tracks/mm10/trackDb.RNAseq.ra
$ cat tracks/mm10/trackDb.RNAseq.ra
track simpleTrack
type bed
shortLabel Very Simple track
longLabel Very Simple Track
# this change directory is missing from the users steps but I assume
they went here first?
$ cd tracks/mm10/
$ hgTrackDb . ${DB} trackDb_local ${sqlDir}/trackDb.sql .
$ hgsql -NBe "select * from trackDb_local" mm10
simpleTrack Very Simple track bed Very Simple Track 0 100 0 0 127 127
127 0 0 0 x 1 longLabel Very Simple Track\nshortLabel Very Simple
track\ntrack simpleTrack\ntype bed\n
After that I get a track called "My Simple Track" in the
"experimental" group of my mirror.
If you have any different steps than the ones above please let us know
and we'd be happy to help further!
Thanks,
Christopher Lee
UCSC Genomics Institute
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