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
