[ensembl-dev] Configured BAM and VCF sources

Nick Langridge nickl at ebi.ac.uk
Wed Sep 28 15:50:12 BST 2011


In EG63, load_configured_bam should be present in 
EnsEMBL::Web::ImageConfig::contigviewbottom;
See eg-plugins/common/modules/EnsEMBL/Web/ImageConfig/contigviewbottom.pm

E.g.
package EnsEMBL::Web::ImageConfig::contigviewbottom;

use strict;

sub modify {
   my $self = shift;

   $self->load_configured_bam;
}

1;

On 28/09/2011 14:14, Nick Langridge wrote:
> Hi Fedor,
>
> Below is a configured BAM example. Note also that you should remove 
> eg-plugins/bam (if you are still using it) this is no longer required 
> - the BAM code has been integrated with Ensembl webcode.
>
> [ENSEMBL_INTERNAL_BAM_SOURCES]
> Puccinia_triticina_SRR035315 = regulation
>
> [Puccinia_triticina_SRR035315]
> source_name        = Transcriptomics sequencing on Puccinia triticina
> description        = RNA-Seq study.
> source_url         = /path/to/bam/files/SRR035315_GG705475.bam
> source_type        = rnaseq
> display            = normal
>
>
> Cheers,
> Nick
>
> On 28/09/2011 13:29, Fedor Gusev wrote:
>> Hello everyone!
>>
>> Can someone provide and example on adding configured BAM and VCF 
>> sources?
>>
>> We had some BAMs attached on release 61 installation, but after
>> upgrading to release 63 they are not displayed anymore. It seems like
>> configuration should be changed (at least name ->  source_name and url
>> ->  source_url). If so, what is the new syntax for those?
>>




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