Hi there, This is my first time writing to the mailing list. Thanks in advance. I want to use Map with BWA for short reads https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=25bdd3c7f0d57b06&tool_config=database%2Fcommunity_files%2F000%2Frepo_253%2Fbwa_wrapper.xml&changeset_revision=b4427dbb6ced (I have added the lines in PS (below) to the section I made in config/tool_conf.xml file and "Map with BWA" is showing up on galaxy interface when I execute run.sh. ) However, I can't pick a genome in the "Using reference genome" box. The drop-down box doesn't work. I have loaded genomes and created indexes to my local galaxy. I just don't know where to insert the path in this file - shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml<http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml> I see it has "reference_fasta_filename" (reference genome) but I am not sure what it is directing to or what to modify to tell where I put the genomes. Or is there something else I need to do? Regards, Ying PS <tool file="../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml<http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml>" guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2<http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2>"> <tool_shed>toolshed.g2.bx.psu.edu<http://toolshed.g2.bx.psu.edu></tool_shed> <repository_name>bwa</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>051eba708f43</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2<http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2></id> <version>0.7.15.2</version> </tool>