Hi Angie and Hiram, Clearing out bai files does help and fixes my issue. Thanks a lot.
As about the mirror, our mirror was created by directly using the binaries downloaded from UCSC server, not by compiling the source. Does that mean KNETFILEHOOKS was already applied? How do we check if our mirror had the patch applied or not? 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
