On 09/12/2014 05:11 PM, Calvin Morrison wrote:
The stderr and stdout is empty, according to galaxy.

here is paster.log output for quikr when i run it.

galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if
user == "user"   quikr -v -k 0 -s
/data/galaxy/galaxy-dist/database/files/000/dataset_103.dat -i
/data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o
/data/galaxy/galaxy-dist/database/files/000/dataset_104.dat   # else
quikr -v -k 0 -s
"/data/galaxy/galaxy-dist/database/files/000/dataset_103.dat".mat.gz -i
/data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o
/data/galaxy/galaxy-dist/database/files/000/dataset_104.dat    # end if

that doesn't really seem all that helpful though.

Actually, it is very helpful, isn't-t? It shows that the command tag from your xml file is not properly executed.

                my xml file:


                     # if $qdb.dbtype == "user"
                     quikr -v -k 0 -s ${qdb.dbname} -i ${input} -o ${output}
                     # else
                     quikr -v -k 0 -s
                "${qdb.dbname}${qdb.dbsize}".__mat.gz -i ${input} -o
                     # end if


try removing the spaces between "#" and "if", "#" and "else", and "#" and "end if". And re-load the tool configuration.

See also: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cwhen.3E_tag_set

Hope this helps

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