I want to make a pipeline that grabs a reference genome, indexes it, then aligns reads to it via bwa. The bwa tool has a menu option for using an index "from the history" (see attached image) but I don't see any option within the bwa wrappers to actually create an index on the fly. This is also true for samtools and other aligners. The following link describes the conf/loc files required to add indexes to the system:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup But how can they be created dynamically in the course of a pipeline run instead of preconfigured in this way? Regards - Joshua
<<attachment: galaxy_bwa_index_input.jpg>>
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
