[ensembl-dev] Attaching BAM sources

Anne Parker ap5 at sanger.ac.uk
Fri Apr 20 09:20:25 BST 2012

Hi Aaron

Which version of Ensembl are you using? I strongly recommend using the latest version and keeping it up-to-date, as we do fix bugs after release. 

1. The BAM file we use to test new releases has a tilde in the URL, so this bug has already been dealt with.

2. Object::UserData used to use the call 


at line 123, as per your error message. However this is commented out in the latest version and now calls

Bio::DB::Sam->new( -bam => $url)

This strongly suggests to me that your Ensembl installation is out-of-date.



On 20 Apr 2012, at 07:40, Aaron Chuah wrote:

> Greetings folks,
> I would appreciate some help after trying unsuccessfully to add local BAM and VCF files despite indexing them according to the instructions. I've attempted both the Attach Remote File method, and trying to edit DEFAULTS.ini and Homo_sapiens.ini in the various directories.
> So far, google has turned up these postings 
> http://lists.ensembl.org/pipermail/dev/2011-March/001059.html
> http://comments.gmane.org/gmane.science.biology.ensembl.devel/8274
> But I've attempted both (with their slightly different forms "source_name" vs "name") but haven't been able to get both my BAMs and VCFs to show.
> Initial attempts to include an external track via URL were foiled by the regular expression parser (which didn't allow tildes which were part of my home directory public_html) -- which should be filed as a separate bug report, but after correcting that,
> http://gdudev.anu.edu.au/data/A.bam open: Bad file descriptor at /usr/local/ensembl/modules/EnsEMBL/Web/Object/UserData.pm line 123.
> Failed to open BAM http://gdudev.anu.edu.au/data/A.bam at /usr/local/ensembl/modules/EnsEMBL/Web/Object/UserData.pm line 133.
> Failed to open BAM index for http://gdudev.anu.edu.au/data/A.bam at /usr/local/ensembl/modules/EnsEMBL/Web/Object/UserData.pm line 134.
> I've tried to circumvent the hostname lookup since it was local via
> open: Bad file descriptor at /usr/local/ensembl/modules/EnsEMBL/Web/Object/UserData.pm line 123.
> Failed to open BAM at /usr/local/ensembl/modules/EnsEMBL/Web/Object/UserData.pm line 133.
> Failed to open BAM index for at /usr/local/ensembl/modules/EnsEMBL/Web/Object/UserData.pm line 134.
> Thanks for your time, as I'd really appreciate help on getting these up.
> Cheers,
> Aaron Chuah
> Genome Discovery Unit
> John Curtin School of Medical Research
> Australian National University
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Anne Parker
Ensembl Web Production Manager

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