Good Morning Tiandao:
What do you see if you dump the contents of your trackDb_wigExample table:
mysql> select tableName from trackDb_wigExample;
While viewing your genome browser where you expect the track to appear,
take a look at your Apache error logs to see if there are any unusual
errors being printed out.
When viewing your genome browser, add this variable JKSQL_TRACE=on to the URL in
your WEB browser address:
http://your.domain.com/cgi-bin/hgTracks?db=hg18&JKSQL_TRACE=on
Take a look at your Apache error log and see if there are any SQL operations
begin performed with your trackDb_wigExample table.
--Hiram
Tiandao Li wrote:
> Hi,
>
> We installed a local genome browser with minimal installation. I tried to
> load wig files to local database.
>
> First, use wigEncode to make wig/wib files.
>
> l...@test01:~$ wigEncode PolII_eland_sorted2.wig PolII.wig PolII.wib
> Converted PolII_eland_sorted2.wig, upper limit 4385.00, lower limit 2.00
>
> 2. mkdir wib folder inside of /mnt/nfs/genomdata/gbdb/hg18/
>
> 3. [l...@research ~]$ /opt/kent/hgLoadWiggle
> -pathPrefix=/mnt/nfs/genomdata/gbdb/hg18/wib hg18 wigExample PolII.wig
> Connected to database hg18 for track wigExample
> Creating wiggle table definition in hg18.wigExample
> Saving wiggle.tab
> WARNING: Exceeded chrM size 16624 > 16571. dropping 3 data point(s)
> Loading hg18
>
> 4. [l...@research ~]$ cp PolII.wib /mnt/nfs/genomdata/gbdb/hg18/wib/
>
> 5. [l...@research trackDb]$ cd bin/kent/src/hg/makeDb/trackDb
> [l...@research trackDb]$ /opt/kent/hgTrackDb human hg18 trackDb_wigExample
> ../../lib/trackDb.sql .
> ....
> ....
> Loaded 4374 track descriptions total
> Loaded database hg18
>
> 6. [l...@research trackDb]$ /opt/kent/hgFindSpec human hg18
> hgFindspec_wigExample ../../lib/hgFindSpec.sql .
> found include file: ./human/hg18/trackDb.chainNet.ra
> found include file: ./human/hg18/trackDb.encode.ra
> found include file: ./human/hg18/trackDb.encodeGenes.ra
> found include file: ./human/hg18/trackDb.encodeTxLevels.ra
> found include file: ./human/hg18/trackDb.encodeChip.ra
> found include file: ./human/hg18/trackDb.encodeChrom.ra
> found include file: ./human/hg18/trackDb.encodeCompAndVar.ra
> found include file: ./human/hg18/trackDb.wgEncode.ra
> found include file: ./human/hg18/wgEncodeRikenCage.alpha.ra
> found include file: ./human/hg18/wgEncodeRikenCage.beta.ra
> found include file: ./human/hg18/wgEncodeCaltechRnaSeq.alpha.ra
> found include file: ./human/hg18/wgEncodeCaltechRnaSeq.beta.ra
> found include file: ./human/hg18/wgEncodeGisPet.alpha.ra
> found include file: ./human/trackDb.encode.ra
> found include file: ./human/trackDb.chainNet.ra
> found include file: ./trackDb.chainNet.ra
> Loaded 216 search specs total
> Loaded database hg18
>
> 7. [l...@research trackDb]$ locate hg.conf
> /var/www/html/genomebrowser/cgi-bin/hg.conf
>
> vim /var/www/html/genomebrowser/cgi-bin/hg.conf
>
> change db.trackDb to
>
> db.trackDb=trackDb_wigExample,trackDb
>
> Now, I open local genome browser, still can't see my wigExample file.
>
> mysql> show tables;
> | wigExample |
> | xenoEst |
> | xenoMrna |
> | xenoRefFlat |
> | xenoRefGene |
> | xenoRefSeqAli |
> | yaleBertoneTars |
> +------------------------------------------------------------------+
>
> mysql> select tableName from trackDb;
>
> | wgEncodeYaleChIPseqViewPeaks |
> | wgEncodeYaleChIPseqViewSignal |
> | wgRna |
> | xenoEst |
> | xenoMrna |
> | xenoRefGene |
> | yaleBertoneTars |
> +------------------------------------------------------------------+
>
> Any help appreciate!!!
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