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 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 ==> "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