When you are in the trackDb directory, to run the make,
use the option CVS=echo
$ make CVS=echo alpha DBS=hg18
Or edit kent/src/inc/common.mk and set the CVS variable
there to echo.
--Hiram
WANG Wuqi wrote:
> Hi Brooke Rhead,
>
> Thanks a lot you and Hiram for support.
>
> I downloaded new version 198 source and upgraded our GBrowsre
> successfully,
> data loading is ok, an new track entry is added to trackDb.ra, but when
> 'make' new DB by command:
> make alpha DBS=hg18
> to encounter error below:
> -----------------------------------------------------------------
> find . -type l -exec rm {} \;
> cvs -q up -d -P .
> cvs update: No CVSROOT specified! Please use the `-d' option
> cvs [update aborted]: or set the CVSROOT environment variable.
> make: *** [alpha] Error 1
> -----------------------------------------------------------------
>
> So I had to remove new directory ~/trackDb and copy old directory
> ~/trackDb,
> then add new track entry to trackDb.ra and 'make alpha DBS=hg18' again,
> this time is ok.
> I want to know that this is a correct solution?
>
>
> Thanks & Regards
>
> Wuqi
>
>
> -----Original Message-----
> From: Brooke Rhead [mailto:[email protected]]
> Sent: Wednesday, January 21, 2009 9:28 AM
> To: WANG Wuqi
> Cc: OW Jack Ling; [email protected]; Atif SHAHAB
> Subject: Re: [Genome] Genome browser upgrade problems
>
> Hello Wuqi,
>
> Hiram was indeed referring to the src/hg/near/hgNear directory.
> However, if you updated your code today, the fix should already be
> incorporated into your source. (The v198 source was released today:
> http://www.soe.ucsc.edu/pipermail/genome-mirror/2009-January/001106.html
> .)
>
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
>
>
> On 01/16/09 01:21, WANG Wuqi wrote:
>> Hi Hiram,
>>
>>
>>
>> We have some differences( below red text ).
>>
>>
>>
>>> For your work-around, after your 'make install' step, go to
>>> the directory in the source tree:
>>> src/hg/hgNear
>>> and run the two commands:
>>> $ rsync -ar --exclude=CVS/ --exclude=.svn/ --delete hgGeneData \
>>> ${DESTDIR}${CGI_BIN}/hgGeneData/
>>> $ chmod -R a+rX ${DESTDIR}${CGI_BIN}/hgGeneData
>>
>>
>>
>>
>>>>>>>> In our work-around, there is NOT a directory or file
>> 'src/hg/hgNear'.
>>
>>
>>
>>> And in the directory:
>>> src/hg/near/hgNear
>>
>>
>>>>>>>> There is the directory 'src/hg/near/hgNear' in source tree.
>>
>>
>>
>>
>> How should we do for step 1?
>>
>>
>>
>>
>>
>> Thanks & Regards
>>
>>
>>
>> Wuqi
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> WANG Wuqi wrote:
>>
>>> Hi Brooke Rhead,
>>
>>> We download new jksrc packages and upgrade our GBrowser(version 196)
>>> Depending on instruct document "README.building".
>>> After building the CGI binaries, we found to lack some files
>>> in /var/www/cgi-bin, like directories /hgGeneData, /hgNearData and so
>>> on.
>>
>>> We found below 2 errors so far:
>>> ----------------------------------
>>> (1) Can not find genome.ra for taskbar "UCSC Genes" in assembly
>> 'human'
>>
>>> see attachment page 1
>>> (2) For link
>>
> http://ucsc.gis.a-star.edu.sg/cgi-bin/hgGene?hgg_gene=uc004eeg.1&hgg_pro
>>
> t=P49335&hgg_chrom=chrX&hgg_start=82649940&hgg_end=82651431&hgg_type=kno
>>> wnGene&db=hg18&hgsid=1647
>>
>>> see attachment page 2
>>
>>> By the way, old version cgi-bin works fine, so it is rolled back now.
>>
>>
>>> Thanks & regards
>>
>>> Wuqi
>> _______________________________________________
>> Genome maillist - [email protected]
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
Genome maillist - [email protected]
http://www.soe.ucsc.edu/mailman/listinfo/genome
