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!!! >>> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
