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 @@
<param name="indices" type="select" label="Select a reference
genome index set">
- <filter type="multiple_splitter" column="2" separator=","/>
- <filter type="param_value" column="2" ref="input1"
<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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