Good Morning Jay: I would recommending backing out any changes you have made in the source tree trackDb hierarchy. Restore your trackDb tables to be identical to our download copies. There is a newly documented easier way to construct your own tracks without working in our source tree. See also, in the source tree: http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.trackDb
Construct your own private trackDb_local.ra file somewhere convenient, with the contents: track bsNonCpGPos shortLabel Non-CpG Region +ive longLabel RMAPBS raw out of non-CpG region +ive strand group x priority 8 visibility dense itemRgb on type bed 9 . Load that into your own private trackDb table called: trackDb_local with the command: hgTrackDb . hg19 trackDb_local $HOME/kent/src/hg/lib/trackDb.sql Adjust that pathname to the file trackDb.sql to be correct for your setup there. Then, in your cgi-bin/hg.conf file, alter the db.trackDb definition line to read: db.trackDb=trackDb_local,trackDb This will use your special table trackDb_local in addition to the normal one from the source tree. You have mthy as a group designation ? Have you constructed a special grp entry for that ? You can do the same trick with the grp table as mentioned above with the trackDb table for your own local grp definitions. Look into the comments in the hg.conf file for the grp line just like this trackDb line. This keeps all of your local changes out of the UCSC tables so database updates will not destroy your local work. --Hiram Jaysheel Bhavsar wrote: > Hey guys, > So it seems that make trackDb isn't working as expected or my syntax is > incorrect. I have following in my trackDb.ra > > ------------------------------------------------------------------------------------ > track cpgMeth > shortLabel CpG Methylation > longLabel RMAPBS CpG Methylation Ratio > group mthy > priority 4 > visibility full > color 102,51,0 > type bedGraph > minLimit 0 > maxLimit 100 > yLineMark 10.0 > yLineOnOff on > > track ncpgpos > shortLabel Non-CpG +ive > longLabel RMAPBS Non-CpG region positive strand > group mthy > priority 6 > visibility dense > type bed 9 . > itemRgb on > ------------------------------------------------------------------------------------ > > after running > >> make alpha GENOMENAME DBNAME trackDb.sql > > I get trackDb.tab file but in this there is no reference for itemRgb, > minLimit, maxLimit, yLineMark and yLineOnOff. Shooting in the dark, I added > 'itemRgb on' in trackDb.settings field and it worked, but I can't seem to get > the settings for bedGraph. My max graphing bound is always 1000. > > Help... > > Thanks > Jay _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
