[ensembl-dev] Attaching BAM sources

[Anne Parker]

On Mon Apr 30 05:45:24 2012, chuah.aaron at gmail.com wrote:

> My queries, thus, are (failing to find more complete documentation
> online):
> 1) What's the "official" way to include a (local) BAM/VCF file as a
> custom
> track for a particular organism? (I've made sure the accompanying
> indices
> are in the same directory.) Do I modify the species configuration ini
> within public-plugins, or is there some other means?

At the moment we configure local BAM tracks using the data_file table in the appropriate database. For example if you look at pan_troglodytes_rnaseq_66_124:

mysql> select * from data_file;
+--------------+-----------------+-------------+-------------------------+--------------+----------+------+-----------+
| data_file_id | coord_system_id | analysis_id | name                    | version_lock | absolute | url  | file_type |
+--------------+-----------------+-------------+-------------------------+--------------+----------+------+-----------+
|            1 |               3 |           3 | C1_herman_br_r1_sorted  |            0 |        0 | NULL | BAM       |
|            2 |               3 |           4 | C2_Japie_br_r1_sorted   |            0 |        0 | NULL | BAM       |
|            3 |               3 |           5 | C5_koos_br_r1_sorted    |            0 |        0 | NULL | BAM       |
|            4 |               3 |           6 | C6_antoine_br_r1_sorted |            0 |        0 | NULL | BAM       |
|            5 |               3 |           7 | merged_sorted           |            0 |        0 | NULL | BAM       |
|            6 |               3 |           8 | introns_sorted          |            0 |        0 | NULL | BAM       |
+--------------+-----------------+-------------+-------------------------+--------------+----------+------+-----------+


These are used in conjunction with a path setting in your DEFAULTS .ini:

DATAFILE_BASE_PATH             = '/path/to/my/files/';

You will also need track definitions in the analysis table of the same database.

We are in the process of implementing simpler methods of configuring these large tracks, but they are not available in release 66.

>
> 2) Failing that, and having to resort to attaching a remote file via
> the
> UI, how may I debug the loading process to ascertain the point of
> failure?
> Just looking into the http error logs have not been too informative.

I suggest putting warns into Bio::EnsEMBL::ExternalData::BAM::BAMAdaptor (in ensembl-external), since the problem seems to be in reading the file rather than displaying it.

Hope this helps

Anne

-- 


Anne Parker
Ensembl Web Production Manager
Anne Parker
Ensembl Web Production Manager
http://www.ensembl.org