[ensembl-dev] Attaching BAM sources

[Nick Langridge]

Hi Fedor,

This may not be relevant, but we had a segfault problem with samtools in 
the past when the http_proxy environment variable is not set correctly. 
If your server uses http_proxy make sure to set the following in 
SiteDefs.pm:

$SiteDefs::SAMTOOLS_HTTP_PROXY = 'http://your.proxy.com';

> And this does not help me with ENSEMBL_INTERNAL_BAM_SOURCES section.
The following example would add a BAM track that will be listed under 
the Information menu in the Main Panel tab when configuring your data.

[ENSEMBL_INTERNAL_BAM_SOURCES]
CTRL = information

[CTRL]
name        = CTRL
description = Control cDNA tag library from David et al. (2010)
url         = /path/to/bam/files/CTRL.fastq.sorted.bam
display     = normal

Cheers,
Nick

On 24/03/2011 13:57, Fedor Gusev wrote:
> 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.
>>
>>      
>
>
>