Hi Hiram,
If I understand your email, and the README files correctly all
trackDb_local.ra will do is keep my tracks in a diff table from that comes with
the src file. Which is all well and good, but the problem that I am facing is
that when I run hgTrackDb weather on trackDb_local.ra or on trackDb.ra (edited
with my tracks). The resulting trackDb_local.tab or trackDb.tab does not have
any reference of the settings for a give track. I have passed -settings
argument to hgTrackDb, but result is the same, the last column in trackDb.tab
or trackDb_local.tab is always empty.
Can you send me an example of what can be in settings field of trackDb.
Specifically I need settings for bedGraph where yLineMark is set to 10,
yLineOnOff is on, vertical viewing range is from 0 to 100.
some guess work I tried which has been unsuccessful so far are:
- If settings field in trackDb starts with 'minLimit 0, maxLimit 100' I
get an error "invalid double 0, maxLimit"
- If settings field in trackDb starts with 'yLineMark 10, yLineOnOff',
I see y=10 under track settings for a given track but on/off drop down is
always off.
- If settings field in trackDb starts with 'yLineOnOff, yLineMark 10'
everything has default values, when viewing track settings.
Jaysheel
p.s: I do have 'mthy' entry in grp table.
On Apr 12, 2010, at 1:02 PM, Hiram Clawson wrote:
> 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
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