[galaxy-dev] Problem with executing newly installed tools (via admin)

8 Apr 2014

      Ok,

a small update on this problem.
I have set up a local tool shed with in it a repository that holds 2 
tool definitions of the same tool but with different verision nbrs

<tool id="NicybDummyTool" name="Nicyb Dummy Tool" version="1.0">
   <description>Dummy Tool</description>
   <command interpreter="python">
     dummyTool.py $inputFile $operand $outputFile
   </command>

   <inputs>
     <param name="inputFile" type="data" format="txt" label="Input txt 
file" />
     <param name="operand" type="text" size="2" label="Operand"/>
   </inputs>

   <outputs>
     <!--callpeaks output-->
     <data name="outputFile" format="txt" label="${tool.name}: output" />
   </outputs>

   <tests>
     <test>
       <param name="inputFile" value="dummyTool_input.txt" ftype="txt"/>
       <param name="operand" value="2"/>
       <output name="outputFile" file="dummyTool_output.txt"/>
     </test>
   </tests>

and:

<tool id="NicybDummyTool" name="Nicyb Dummy Tool" version="2.0">
   <description>Dummy Tool v2</description>
   <command interpreter="python">
     dummyTool_v2.py $inputFile $operand $outputFile
   </command>

   <inputs>
     <param name="inputFile" type="data" format="txt" label="Input txt 
file" />
     <param name="operand" type="text" size="2" label="Operand"/>
   </inputs>

   <outputs>
     <!--callpeaks output-->
     <data name="outputFile" format="txt" label="${tool.name}: output" />
   </outputs>

   <tests>
     <test>
       <param name="inputFile" value="dummyTool_input.txt" ftype="txt"/>
       <param name="operand" value="2"/>
       <output name="outputFile" file="dummyTool_output_v2.txt"/>
     </test>
   </tests>

</tool>

</tool>

I am successful in installing these tools in Galaxy using out own toolshed.
I get the following lines in shed_tool_conf.xml

<section id="nicyb_test_3" name="nicyb test 3" version="">
   <tool 
file="galaxy.psb.ugent.be/repos/nicyb/testbla2/4c7117d7f90d/testbla2/dummyTool_wrapper.xml" 
guid="galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/1.0">
<tool_shed>galaxy.psb.ugent.be:3333/toolshed</tool_shed>
         <repository_name>testbla2</repository_name>
         <repository_owner>nicyb</repository_owner>
<installed_changeset_revision>4c7117d7f90d</installed_changeset_revision>
<id>galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/1.0</id>
         <version>1.0</version>
     </tool>
     <tool 
file="galaxy.psb.ugent.be/repos/nicyb/testbla2/4c7117d7f90d/testbla2/dummyTool_wrapper_v2.xml" 
guid="galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/2.0">
<tool_shed>galaxy.psb.ugent.be:3333/toolshed</tool_shed>
         <repository_name>testbla2</repository_name>
         <repository_owner>nicyb</repository_owner>
<installed_changeset_revision>4c7117d7f90d</installed_changeset_revision>
<id>galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/2.0</id>
         <version>2.0</version>
     </tool>
</section>

When I look in the tool panel I can see both tools under section nicyb 
test3.
Upon selecting one I get Nicyb Dummy Tool and then a drop down with 
"version 1.0" and "version 2.0"
However, when I change the version nbrs I get the following error:

  Module MySQLdb.connections:36 in defaulterrorhandler         view
OperationalError: (OperationalError) (1241, 'Operand should contain 1 
column(s)') 'INSERT INTO event (create_time, update_time, history_id, 
user_id, message, session_id, tool_id) VALUES (%s, %s, %s, %s, %s, %s, 
%s)' (datetime.datetime(2014, 4, 8, 14, 34, 48, 567645), 
datetime.datetime(2014, 4, 8, 14, 34, 48, 567654), 1L, 1L, "Tool params: 
{'operand': u'', 'tool_state': 
u'800255db313334303737356537316139353463626339613333356235633261356166623236313166623137643a3762323236663730363537323631366536343232336132303232356332323465366636653635356332323232326332303232356635663730363136373635356635663232336132303330326332303232356635663732363537323735366535663732363536643631373035663661366636323566363936343566356632323361323036653735366336633263323032323639366537303735373434363639366336353232336132303232333233323232376471002e', 
'refresh': u'refresh', 'inputFile': u'22'}", 16L, 
[u'galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/2.0', 
u'galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/1.0'])

Is there anyone with similar experiences or an explanation for this ?

Kind regards,

Nicolas

On 04/02/2014 06:00 PM, galaxy-dev-request@lists.bx.psu.edu wrote:
...
Subject:
[galaxy-dev] Problem with executing newly installed tools (via admin)
From:
"Nicolas Cybulski" <nicyb@psb.vib-ugent.be>
Date:
04/02/2014 10:38 AM
To:
galaxy-dev@lists.bx.psu.edu
Hi,
I have installed the Picard tools using the Tool-shed functionality in 
the admin tools.
The tools and requisites have been correctly installed and run correctly.
The insert statement to the event table fails however. I get the 
following error on screen:
|OperationalError: (OperationalError) (1241, 'Operand should contain 1 
column(s)') 'INSERT INTO event (create_time, update_time, history_id, 
user_id, message, session_id, tool_id) VALUES (%s, %s, %s, %s, %s, %s, 
%s)' (datetime.datetime(2014, 4, 2, 9, 32, 47, 823142), 
datetime.datetime(2014, 4, 2, 9, 32, 47, 823170), 35L, 4L, "Tool 
params: {'histWidth': u'0', 'deviations': u'10.0', 'malevel': 
u'ALL_READS', 'input_file': u'5266', 'out_prefix': u'Insertion size 
metrics', 'refresh': u'refresh', 'minPct': u'0.05', 'tool_state': 
u'800254cf010000316164663833323133363237333739303833323639353065346362343762393730383966363664313a37623232363836393733373435373639363437343638323233613230323235633232333035633232323232633230323236343635373636393631373436393666366537333232336132303232356332323331333032653330356332323232326332303232363936653730373537343566363636393663363532323361323032323335333233363336323232633230323235663566373036313637363535663566323233613230333032633230323235663566373236353732373536653566373236353664363137303566366136663632356636393634356635663232336132303665373536633663326332303232366436313663363537363635366332323361323032323563323234313463346335663532343534313434353335633232323232633230323236663735373435663730373236353636363937383232336132303232356332323439366537333635373237343639366636653230373336393761363532303664363537343", 
1468L, 
[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0', 
u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0'])
|The problem seems to be a duplicate entry of the tool_id
|[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0', 
u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0']
|In the shed_tool_conf.xml the tools are generated as follows
<tool 
file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardInsertSize.xml"guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0">
If I change this guid to something less complicated like
<tool 
file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardInsertSize.xml" 
guid="testPicard">
and restart galaxy it works ...
for all tools (so not only the one that I've changed).
Does anyone have an idea as to why this is ?
kind regards,
Nicolas