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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