Hi Duke, Yes, the hg* CGI programs will need to be recompiled, also with KNETFILE_HOOKS=1. But if your local admin is willing to "rm /usr/local/apache/trash/samtools/*.bai", that should take only a few seconds and it might clear up the problem.
If you do recompile, here's a way to cut some corners, just for this case (rebuild only the CGI programs, not command-line utils): [first set up the build environment variables, including KNETFILE_HOOKS=1] cd kent/src/hg make clean make libs make compile Then ask your local admin to "cd kent/src/hg; make install". "make compile" does not install programs in apache/cgi-bin, but instead leaves them in the source directories (kent/src/hg/hg*/), and I'm hoping you have the file permissions to modify files in the source directories. Hope that helps, Angie ----- "Duke" <[email protected]> wrote: > From: "Duke" <[email protected]> > To: "Hiram Clawson" <[email protected]> > Cc: [email protected] > Sent: Monday, November 22, 2010 1:58:42 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] empty data for BAM tracks > > Hi Hiram, > > I am sorry I am still not clear. What I meant was would the > KNETFILEHOOKS-recompiled samtool work with the old local mirror, or we > have to recompile the local mirror as well? The reason is recompiling > the mirror will take quite a bit of time, and we need to contact our > local admin to do that. > > Thanks, > > D. > > On 11/22/10 4:47 PM, Hiram Clawson wrote: > > You can use the scripts in the source tree: src/product/scripts/ > > to build your kent source tree. > > > > > > ----- Original Message ----- > > From: "Duke"<[email protected]> > > To: "Angie Hinrichs"<[email protected]> > > Cc: [email protected], "Hiram Clawson"<[email protected]> > > Sent: Monday, November 22, 2010 1:35:23 PM GMT -08:00 US/Canada > Pacific > > Subject: Re: [Genome] empty data for BAM tracks > > > > Hi Angie, > > > > No, I dont use KNETFILE_HOOKS and I believe our local mirror was > not > > built with that option as well. But our samtools and mirror have > been > > working just fine until I encouter that issue. I am gonna apply > that > > patch and rebuild our samtools, but does that mean we have to ask > our > > local admin to recompile (or apply batch) to the genome code as > well? > > > > Thanks, > > > > D. > > > > > > On 11/22/10 11:43 AM, Angie Hinrichs wrote: > >> Hi Duke, > >> > >> Did you compile your samtools and kent/src with KNETFILE_HOOKS=1 ? > (That requires downloading and applying a patch to the samtools > source, see http://genomewiki.ucsc.edu/index.php/KNETFILE_HOOKS .) If > so, is it possible to make a small test file that has the same > problem, and put it on a public site or email to me for debugging? > >> > >> If you didn't use KNETFILE_HOOKS, then empty bam track can be > caused by stale index files (.bam.bai) that the samtools C library > saves in a local directory. To clear all index files, "rm > ${TRASHDIR}/samtools/*.bai" . Depending on your installation, > TRASHDIR is probably something like /usr/local/apache/trash . If the > track is still blank after clearing the index files, please send a > test case, or try "samtools view my.bam chr1:2-3" where chr1:2-3 is > the region you are viewing in the browser. > >> > >> Hope that helps, > >> Angie > >> > >> ----- "Duke"<[email protected]> wrote: > >> > >>> From: "Duke"<[email protected]> > >>> To: "Hiram Clawson"<[email protected]> > >>> Cc: [email protected] > >>> Sent: Saturday, November 20, 2010 6:08:56 AM GMT -08:00 US/Canada > Pacific > >>> Subject: Re: [Genome] empty data for BAM tracks > >>> > >>> On 11/19/10 8:33 PM, Hiram Clawson wrote: > >>>> Take a look in your Apache error log files to see if there > >>>> are any error messages about your track from the browser CGI > >>>> binaries. The messages should have appeared when you loaded > >>>> the tracks, but maybe something else is going wrong. > >>> Thanks Hiram for your suggestion. I have contacted our local admin > about > >>> that. Aside from the admin side, based on your experience, is > there any > >>> other reason from the user side that can cause the issue? > >>> > >>> Thanks, > >>> > >>> D. > >>> > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
