Hi Hans, This was a change in the Cheetah syntax, which changed in a recent version. You have found the correct fix, and thanks for pointing out the wiki page, which I've fixed. --nate Hotz, Hans-Rudolf wrote:

Hi

(I am sorry, if this has been reported already, but I couldn't find it in the archive)

This morning, I upgraded one of our local galaxy servers from changeset 2833 to 3545....so far, I haven't encountered any major problems, except for the cases, where we use a conditional, eg:

<command> #if $range.mode=="part":#clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_format1 -SEQNOS=$out_format2 -RANGE=$range.seq_range_start,$range.seq_range_end #else :#clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_format1 -SEQNOS=$out_format2 #end if </command>

which is pretty much the same as the example for the <conditional> tag set in the wiki (ToolConfigSyntax):

<command interpreter="python"> #if $source.source_select=="database":#blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off #else:#blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off #end if </command>

However, I got the following error (after the upgrade):

//// File "/work2/scratch/galaxy/galaxy_dist/eggs/Cheetah-2.2.2-py2.5-linux-x86_64-ucs 4.egg/Cheetah/Parser.py", line 2645, in popFromOpenDirectivesStack raise ParseError(self, msg="#end found, but nothing to end") ParseError:

#end found, but nothing to end Line 4, column 1

Line|Cheetah Code ----|------------------------------------------------------------- 2 | #else:#clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_format1 -SEQNOS=$out_format2 3 | #end if 4 | ^ ////

after looking around in similar tool config files which have been changed in the distribution, I noticed that the colons are no longer present. I removed both ":" in front of "#clustalw2", resulting in:

<command> #if $range.mode=="part" #clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_format1 -SEQNOS=$out_format2 -RANGE=$range.seq_range_start,$range.seq_range_end #else #clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_format1 -SEQNOS=$out_format2 #end if </command>

and it worked!

was this the correct fix? and if so, could you please update the wiki page, ie removing the two ":" in front of "#blat_wrapper.py"

Thank you very much for your help

Hans

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