You will need access to determine what is wrong. Tiandao Li wrote: > I can't access /var/log/httpd/. > > On Thu, May 6, 2010 at 12:18 PM, Tiandao Li <[email protected]> wrote: > >> mysql> select tableName from trackDb_wigExample; >> ......... >> .......... >> | zhaoLabRestingNucleosomeRevWig | >> | zhaoLabRestingUnphosPolII | >> | zhaoLabRestingUnphosPolIIBedGraph | >> +------------------------------------------------------------------+ >> 4374 rows in set (0.01 sec) >> >> I opened our website >> >> http://research.icts.uiowa.edu/genomebrowser/cgi-bin/hgTracks?db=hg18&JKSQL_TRACE=on >> >> looks like nothing changed. >> >> Where should I look for Apache error logs on EL5? >> >> Thanks, >> >> Tiandao >> >> >> On Thu, May 6, 2010 at 12:11 PM, Hiram Clawson <[email protected]> wrote: >> >>> 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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