[ensembl-dev] Attaching BAM sources

[Aaron Chuah]

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
http://127.0.0.1/data/A.bam open: Bad file descriptor at
/usr/local/ensembl/modules/EnsEMBL/Web/Object/UserData.pm line 123.
Failed to open BAM http://127.0.0.1/data/A.bam at
/usr/local/ensembl/modules/EnsEMBL/Web/Object/UserData.pm line 133.
Failed to open BAM index for http://127.0.0.1/data/A.bam 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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