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.zeitouni@curie.fr

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