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"/>

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 Briggs peter.bri...@manchester.ac.uk
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