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" error I see on my error-log. That can only
be relative to the gz -> bed pipe, whereby the hgCustom script aborts as
soon as it "sees" that the expected package has not arrived in its
entirety. Since it seems 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 for me to solve this issue? I was thinking of
having the script to "wait" for the whole package to "arrive" rather
than abort, but don't know whether I should tweak customfactory.c or any
other library.
To refresh the memory:
- 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 as a custom track
- gz version of same file is not.
- errors:
"Error File 'test.bed.gz' - Operation not permitted error from
setpgid(6585, 6584)"
"Can't start query: select genome from dbDb where name = 'mm9' mySQL
error 2006: MySQL server has gone away
Thanks a lot!
Fred
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 :)
--
Federico De Masi, PhD,
Assistant Professor
The Technical University of Denmark - DTU
Center for Biological Sequence Analysis - CBS
Kemitorvet 208/002
DK-2800 KGS. LYNGBY, DENMARK
Telephone: (+45) 45 25 24 21
Fax: (+45) 45 93 15 85
http://www.rg.cbs.dtu.dk
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