Problem with executing newly installed tools (via admin)

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Problem with executing newly installed tools (via admin)

Nicolas Cybulski
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, [hidden email] wrote:
Subject:
[galaxy-dev] Problem with executing newly installed tools (via admin)
From:
"Nicolas Cybulski" [hidden email]
Date:
04/02/2014 10:38 AM
To:
[hidden email]

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'800254cf010000316164663833323133363237333739303833323639353065346362343762393730383966363664313a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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


___________________________________________________________
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/