Hello
I'm configuring a personal Galaxy instance with NGS tools (precursor to setting up a local production version) and had some difficulty getting the Bfast mapper (NGS Mapping -> Map with BFAST) to pick up the reference genomes from the bfast_indexes.loc file.
I'm using a hg clone of galaxy-dist, and declared the reference indexes in tab-delimited format, as indicated by the comments in bfast_indexes.loc.sample. However the bfast_wrapper.xml seems to expect some kind of comma-separated value? Anyway patching bfast_wrapper.xml thusly fixed the problem for me:
--- bfast_wrapper.xml.orig 2011-06-23 09:56:54.008898765 +0100 +++ bfast_wrapper.xml 2011-06-23 10:01:30.048840835 +0100 @@ -62,8 +62,6 @@ <when value="indexed"> <param name="indices" type="select" label="Select a reference genome index set"> <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>
I can imagine that using a different format in bfast_indexes.loc should also work, but tab-delimited seems more consistent with the other loc files.
Apologies if this is a known issue (I couldn't find anything in the GMOD archive, and neither bfast_wrapper.xml or bfast_indexes.loc.sample seem to have changed wrt this issue in Galaxy Central), or if I've missed something really obvious.
Thanks for your help, best wishes
Peter