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 è /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 tools/sr_mapping/bfast_wrapper.xml:

<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" ref_attribute="extension"/>

            <filter type="sort_by" column="3"/>

            <validator type="no_options" message="No indexes are available for the selected input dataset"/>

          </options>

        </param>

      </when>

And the bfast_indexes è “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    /galaxyIndices/genomes/Ecoli/eschColi_K12/bfast/eschColi_K12.fa

Any suggestions?

Look forward to your reply.

Best regards,

Sean