Hi Duke, Glad to hear you can see your data now! I think KNETFILE_HOOKS should have been applied to our released binaries, but I will have to double-check. Do you remember how long ago you downloaded the binaries (or can your local admin ls -l to see the file dates)?
Angie ----- "Duke" <[email protected]> wrote: > From: "Duke" <[email protected]> > To: "Angie Hinrichs" <[email protected]> > Cc: [email protected], "Hiram Clawson" <[email protected]> > Sent: Tuesday, November 23, 2010 9:48:39 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] empty data for BAM tracks > > 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
