I am trying to install and configure a local galaxy server for our research team. I have set up a Virtual Ubuntu 11.10 played by VirtualBox and installed galaxy using this tutorial. It amazes me that I cannot find the option to do BWA-alignment for short Illumina reads. According to the wiki there should be $GALAXY_PATH/tools/sr_mapping/bwa_wrapper.xml and $GALAXY_PATH/tool-data/bwa_index.loc which are both not present. Furthmore, when I look in the $GALAXY_PATH/tool_conf.xml in the section "NGS: Mapping" there is no record of <tool file="sr_mapping/bwa_wrapper.xml"/>
Where can I find a bwa_wrapper.xml and bwa_wrapper.py so that I can use it in my local galaxy server?