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!!!
>>>
>
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