Bruno Zeitouni wrote:
> Dear all,
> 
> I would like to use our built-in color-spaces indexes for BWA with
> Galaxy but I failed to do it.
> 
> I added the following line in the "bwa_index_color.loc" file of the
> "tool-data" directory :
> 
> hg19   hg19   hg19             my_path_to/hg19.fa
> 
> but I don't see the reference hg19 appeared onto the browser... ("Map
> with BWA for SOLiD")

Hi Bruno,

the BWA for SOLiD tool uses the bwa_indexes_color data table, so first,
ensure that its definition appears in tool_data_table_conf.xml:

    <table name="bwa_indexes_color" comment_char="#">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/bwa_index_color.loc" />
    </table>

And then add your indexes to the tool-data/bwa_index_color.loc file.

--nate

> 
> Maybe I missed something here because there is a note about the original
> path for hg19 for workflow backwards compatibility (?), but I don't
> understand what it means..
> 
> For the BFAST indexes, It is OK.
> 
> Thank you for your help
> 
> Bruno
> 
> -- 
> 
> Bruno Zeitouni, PhD
> Institut Curie - U900 INSERM - Mines ParisTech
> Equipe Bioinformatique
> Bâtiment de Biologie du Développement
> 26 rue d'ULM
> 75248 Paris Cedex 05 - FRANCE
> 
> Tél  : +33 1 56 24 69 31
> Mail : bruno.zeito...@curie.fr
> 

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