Thanks Angie and Hiram. We are contacting our admin to help us on the issue per your suggestion. Hopefully everything will be sorted out soon.
Thanks, D. On 11/22/10 5:55 PM, Angie Hinrichs wrote: > 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
