Federico, Did you see Hiram's comment that he sent you on 5/23?
"Check to see if you have a system called SElinux installed and functioning. This is "Security Enhanced linux" and can prevent any number of things from functioning: http://en.wikipedia.org/wiki/SElinux --Hiram" - Greg On 5/30/11 6:11 AM, Federico De Masi wrote: > HI again Greg, > thanks for your reply. > Unfortunately /tmp/ has all the proper permissions. That would have been > the easiest fix. But would have also made sense if the system would not > accept any custom track. > > We think that the issue has to do with the "pipeline input buffer short > write 65536, expected 925909, referer: h" error I see on my error-log. > That can only be relative to the gz -> bed pipe created to write into mySQL. > > Since it seem that it is not possible to change that buffer size (at the > kernel level), is there any suggestions you would (or anyone out there) > have? > > To make things clear: > - gz is functioning and recognised by apache2 as a "compressed extension". > - I am running Suse virtual server with a 2.6.34-12-desktop kernel. > - uncompressed bed file is happily loaded > - gz version of same file is not > > Thanks a lot! > > Fred > > PS: heeeeeeeeeeelp!!!! > > On 19/05/2011 22:58, Greg Roe wrote: >> Hi Federico, >> >> I sent this over to one of our mirror experts who had this to say: >> >> "These are very odd error messages. When we see a compressed file, >> we use the command 'gzip' (for .gz files) to uncompress the incoming >> data in a unix pipeline command. This could cause the creation >> of a pipe file handle in the /tmp/ directory which should be writable >> via the Apache process, but maybe they have Apache locked down so it >> can not do that. They may need to check permissions on the /tmp/ >> directory (which should always allow all permissions for any process) >> or they need to check their Apache configuration to see if it has >> some limitation on running unix pipeline commands." >> >> If you make these checks and still have no luck, just let us know: >> [email protected] >> >> - >> Greg Roe >> UCSC Genome Bioinformatics Group >> >> >> On 5/9/11 9:17 AM, Federico De Masi wrote: >>> Dear UCSC devs and users, >>> >>> Before I can deploy my in-house version of the UCSC Browser, I need to >>> tweak the last bit, ie: customTracks. >>> >>> So far, it works a charm when using non compressed files. They load, >>> show up etc etc. As soon as I try to upload a .gz track, all hell breaks >>> lose. >>> I get: >>> >>> - Operation not permitted error from setpgid(8638, 8637) >>> >>> and >>> >>> - Can't start query: >>> select genome from dbDb where name = 'syboss_hg19' >>> - mySQL error 2006: MySQL server has gone away >>> >>> >>> I am pretty sure it has to do with the decompression of the gz file, but >>> I give up. I tried many things, but can't find a solution. >>> >>> Please, help meeeeee :) _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
