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:
<command>
# 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 ${output} # end if
</command>
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_... Hope this helps Hans-Rudolf