Peter,

This loc file is tab-separated, but it's just that one of its columns (the third, which holds the Galaxy formats that the line applies to) can hold comma-separated values. For instance, you could have the line:
hg18_standard hg18 fastqsanger,fastqcssanger hg18 standard indexes /data/hg18/bfast_index/hg18.fa
where these indexes would work for both base- and color-space data. What those two lines of code do is look at the input dataset's extension to see if it matches any of the comma-separated values, and if it does then that line is included in the dropdown box.

So if your file is tab-separated and has the right column values but still isn't showing up, you've got another issue. Do you have a tool_data_table_conf.xml file that contains an entry for "bfast_indexes"? Let us know if you are still having issues.

Thanks,
Kelly


On Thu Jun 23, at 12:11 PM, Peter Briggs wrote:

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

--
Peter Briggs peter.briggs@manchester.ac.uk
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