[ensembl-dev] Attaching BAM sources

[Fedor Gusev]

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.