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_set


Hope this helps

Hans-Rudolf
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Reply via email to