Hi Hiram,
I had a feeling this had to do with delimiter between each settings.
At this time I am forced to add tracks manually, because my version of MySQL
does not allow 'load local infile...' command, default install of mysql 5.1.40
has this feature disabled. I have tried to add options in my.cnf and even
tried to run mysqld with --infile option but for some reason all hg scripts
exit with the error.
Thanks for your patients and input on this, using \n as delimiter I have been
able to get settings to work for now. Hopefully production server wont have
the same issues.
Jay
On Apr 12, 2010, at 2:47 PM, Hiram Clawson wrote:
> Good Morning Jay:
>
> We need to get your hgTrackDb command to load your table. Manually trying
> to load settings into a trackDb table is a quixotic task.
>
> Here is an example:
>
> Here is my .ra file:
> $ cat local.ra
> 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 .
> yLineOnOff on
> yLineMark 10
> minLimit 10
> maxLimit 10
>
> Loading it into a test table:
>
> $ hgTrackDb . hg19 trackDb_test $HOME/kent/src/hg/lib/trackDb.sql .
> -raName=local.ra
>
> The contents of that table: (the cat -A shows all characters
>
> $ hgsql -N -e "select * from trackDb_test;" hg19 | cat
> bsNonCpGPos Non-CpG Region +ive bed 9 . RMAPBS raw out of non-CpG
> region +ive strand 1 8 0 0 0 127 127
> 127 00 0 x 1 group
> x\nitemRgb on\nlongLabel RMAPBS raw out of non-CpG region +ive
> strand\nmaxLimit 10\nminLimit 10\npriority 8\nshortLabel Non-CpG Region
> +ive\ntrack bsNonCpGPos\ntype bed 9 .\nvisibility dense\nyLineMark
> 10\nyLineOnOff on\n
>
> Note, all the settings you wanted are in the settings string.
>
> You should be able to construct a table like this.
>
> The definitions of all the settings allowed are in the trackDb/README file.
> You can find examples of the usage of the settings in the trackDb.ra files
> in the source tree.
>
> --Hiram
>
> Jaysheel Bhavsar wrote:
>> 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
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
