Hello all,

I have been trying to fix the index problem of BFast since last week, somehow, 
the index didn't show in the drop-down box no matter how I managed to modify 
the configurations. I listed my steps in the following, hopefully you can help 
me to point out where the problem is:

Taken one example for Ecoli.
The index files plus a symbolic link of the genome file for Bfast are stored in 
==> /galaxyIndices/genomes/Ecoli/eschColi_K12/bfast
I check the global conf files, tool_conf.xml and tool_data_table_conf.xml, 
which both contain the relevant files (sr_mapping/bfast_wrapper.xml and 
tool-data/bfast_indexes.loc) for bfast.

The index should be displayed through the following codes in 

<when value="indexed">
        <param name="indices" type="select" label="Select a reference genome">
          <options from_data_table="bfast_indexes">
            <filter type="multiple_splitter" column="2" separator=","/>
            <filter type="param_value" column="2" ref="input1" 
            <filter type="sort_by" column="3"/>
            <validator type="no_options" message="No indexes are available for 
the selected input dataset"/>

And the bfast_indexes ==> "tool-data/bfast_indexes.loc", which points to the 
directories where the index files are:
#<unique_id>    <build> <galaxy format extensions valid1,valid2>        
<description>   <bfast_index_directory>
eschColi_K12    eschColi_K12     fastqsanger,fastqcssanger      eschColi_K12    

Any suggestions?

Look forward to your reply.

Best regards,

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