yes, I can zoom in to 1 base and see th DNA sequence. I turned on base position, ucsc genes, refseq genes, and repeatmasker. also can turn Gap on, looks OK to me.
I don't know where is visibility control button? group of buttons? On Thu, May 6, 2010 at 1:23 PM, Hiram Clawson <[email protected]> wrote: > Backing off a little bit. Ignore your special track for the moment. Does > anything > at all show up in your browser screen ? Is the genome browser drawing the > display ? Can you navigate to the "base" view and see the DNA sequence of > the genome in the browser in the base track ? Does the gap track function > properly ? > > Do you see a visibility control button for your track in the genome browser > visibility controls ? Which group of buttons is it in ? > > --Hiram > > > Tiandao Li wrote: > >> Answers from local DBA: >> >> These accesses to trackDb_wigExample are listed in the error_log after I >> visit that page >> >> >> [Thu May 06 12:31:12 2010] [error] [client 129.255.34.208] SELECT 1 FROM >> trackDb_wigExample LIMIT 0 >> [Thu May 06 12:31:12 2010] [error] [client 129.255.34.208] SELECT 1 FROM >> trackDb_wigExample LIMIT 0 >> [Thu May 06 12:31:12 2010] [error] [client 129.255.34.208] select * from >> trackDb_wigExample where tableName = 'chromInfo' >> [Thu May 06 12:31:12 2010] [error] [client 129.255.34.208] SELECT 1 FROM >> trackDb_wigExample LIMIT 0 >> [Thu May 06 12:31:12 2010] [error] [client 129.255.34.208] select * from >> trackDb_wigExample >> >> Without the JKSQL_TRACE=on, I see no entries in the error log. >> >> >> >> On Thu, May 6, 2010 at 12:29 PM, Tiandao Li <[email protected]> wrote: >> >> I contacted local DBA to solve this Apache errors. >>> >>> >>> On Thu, May 6, 2010 at 12:26 PM, Hiram Clawson <[email protected]> >>> wrote: >>> >>> You may find them in: >>>> /var/log/httpd/ >>>> or maybe: /var/www/logs/ >>>> or maybe: /etc/httpd/logs/ >>>> >>>> Something like that. Look for apache conf files in: >>>> /etc/httpd/conf/httpd.conf >>>> the concatenation of ServerRoot and ErrorLog will be the location of >>>> the error log file: >>>> >>>> $ egrep "^ServerRoot|^ErrorLog" /etc/httpd/conf/httpd.conf >>>> >>>> --Hiram >>>> >>>> >>>> Tiandao Li 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
