[ensembl-dev] Attaching BAM sources

[Fedor Gusev]

Apparently, if I run apache in single process mode, everything works
fine, but slow.

And this does not help me with ENSEMBL_INTERNAL_BAM_SOURCES section.

On Thu, Mar 24, 2011 at 1:45 PM, Fedor Gusev <gusevfe at gmail.com> wrote:
> Hello everyone.
>
> I want to attach some BAM tracks to my local ensembl install and i
> have a problem with that.
>
> First, if I attach a BAM file through web interface (providing a url),
> nothing happens and logs show the following:
>
> [Thu Mar 24 13:27:57 2011] [notice] child pid 9988 exit signal
> Segmentation fault (11), possible coredump in /tmp/apache-dumps
> [Thu Mar 24 13:27:57 2011] [notice] child pid 9989 exit signal
> Segmentation fault (11), possible coredump in /tmp/apache-dumps
>
> Segfault happens after line
>        $bam = Bio::DB::Bam->open($url);
> at ./modules/EnsEMBL/Web/Command/UserData/AttachBAM.pm:41
> The dump shows a problem in khttp_connect_file() from samtools.
>
> If i ran the same eval block from a test script, everything looks fine.
> I think there is some kind of apache restrictions on child processes,
> and they need to be configured, but I don't know how.
>
> Second, it seems there is an ENSEMBL_INTERNAL_BAM_SOURCES section in
> ini-files. Does anyone have an example of this?
>
> --
> Kind regards,
> Fedor Gusev.
>



-- 
Kind regards,
Fedor Gusev.