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
_______________________________________________
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