Tool Errors

classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

Tool Errors

Calvin Morrison
Hi guys,

I am trying to write a tool with a conditional and for whatever reason the results, well aren't any results. It just says 'no seek', which totally bewildering. Does anyone know what this means?

Thank you,
Calvin 

my xml file:

<tool id="quikr" name="Quikr">
  <description>Classify with Quikr</description>
  <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>
  <inputs>
    <param name="input" type="data" format="fasta" label="input fasta file"/>
    <conditional name="qdb">
        <param name="dbtype" type="select" label="Genomes to score against">
          <option value="default" selected="true">Pretrained databases</option>
          <option value="user">Custom trained quikr database</option>
        </param>
        <when value="user">
          <param name="dbname" type="data" format="quikrdb" label="custom trained database"/>
          <param name="dbsize" type="hidden" label="mer size">
            <option value="5">5</option>
          </param>
        </when>
        <when value="default">
          <param name="dbname" type="select" label="Choose database">
            <option value="/data/galaxy/data/gg91">Green Genes 91%</option>
            <option value="/data/galaxy/data/gg94">Green Genes 94%</option>
            <option value="/data/galaxy/data/rdp">RDP Trained Set</option>
          </param>
          <param name="dbsize" type="select" label="mer size">
            <option value="5">5</option>
            <option value="6">6</option>
            <option value="7">7</option>
            <option value="8">8</option>
          </param>
        </when>
    </conditional>
    <param name="lambda" type="integer" size="6" value="10000" label="lambda" help="default 10000"/>
  </inputs>
  <outputs>
    <data name="output" format="tabular" />
  </outputs>
  <help>
  </help>
</tool>


___________________________________________________________
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 | Threaded
Open this post in threaded view
|

Re: Tool Errors

Björn Grüning-3
Hi,

as far as I know, it just means your tool did not produced any output,
so your results is empty. Nothing more. This is no error, or? The box is
not red?

Cheers,
Bjoern

Am 12.09.2014 um 16:28 schrieb Calvin Morrison:

> Hi guys,
>
> I am trying to write a tool with a conditional and for whatever reason the
> results, well aren't any results. It just says 'no seek', which totally
> bewildering. Does anyone know what this means?
>
> Thank you,
> Calvin
>
> my xml file:
>
> <tool id="quikr" name="Quikr">
>    <description>Classify with Quikr</description>
>    <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>
>    <inputs>
>      <param name="input" type="data" format="fasta" label="input fasta
> file"/>
>      <conditional name="qdb">
>          <param name="dbtype" type="select" label="Genomes to score against">
>            <option value="default" selected="true">Pretrained
> databases</option>
>            <option value="user">Custom trained quikr database</option>
>          </param>
>          <when value="user">
>            <param name="dbname" type="data" format="quikrdb" label="custom
> trained database"/>
>            <param name="dbsize" type="hidden" label="mer size">
>              <option value="5">5</option>
>            </param>
>          </when>
>          <when value="default">
>            <param name="dbname" type="select" label="Choose database">
>              <option value="/data/galaxy/data/gg91">Green Genes 91%</option>
>              <option value="/data/galaxy/data/gg94">Green Genes 94%</option>
>              <option value="/data/galaxy/data/rdp">RDP Trained Set</option>
>            </param>
>            <param name="dbsize" type="select" label="mer size">
>              <option value="5">5</option>
>              <option value="6">6</option>
>              <option value="7">7</option>
>              <option value="8">8</option>
>            </param>
>          </when>
>      </conditional>
>      <param name="lambda" type="integer" size="6" value="10000"
> label="lambda" help="default 10000"/>
>    </inputs>
>    <outputs>
>      <data name="output" format="tabular" />
>    </outputs>
>    <help>
>    </help>
> </tool>
>
>
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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 | Threaded
Open this post in threaded view
|

Re: Tool Errors

Calvin Morrison
Which me thinks is weird, because my code, when given the -v flag will at least put out some info to stdout, or worse case, some errors to stderr, but those are empty too!

On 12 September 2014 10:31, Björn Grüning <[hidden email]> wrote:
Hi,

as far as I know, it just means your tool did not produced any output, so your results is empty. Nothing more. This is no error, or? The box is not red?

Cheers,
Bjoern

Am 12.09.2014 um 16:28 schrieb Calvin Morrison:
Hi guys,

I am trying to write a tool with a conditional and for whatever reason the
results, well aren't any results. It just says 'no seek', which totally
bewildering. Does anyone know what this means?

Thank you,
Calvin

my xml file:

<tool id="quikr" name="Quikr">
   <description>Classify with Quikr</description>
   <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>
   <inputs>
     <param name="input" type="data" format="fasta" label="input fasta
file"/>
     <conditional name="qdb">
         <param name="dbtype" type="select" label="Genomes to score against">
           <option value="default" selected="true">Pretrained
databases</option>
           <option value="user">Custom trained quikr database</option>
         </param>
         <when value="user">
           <param name="dbname" type="data" format="quikrdb" label="custom
trained database"/>
           <param name="dbsize" type="hidden" label="mer size">
             <option value="5">5</option>
           </param>
         </when>
         <when value="default">
           <param name="dbname" type="select" label="Choose database">
             <option value="/data/galaxy/data/gg91">Green Genes 91%</option>
             <option value="/data/galaxy/data/gg94">Green Genes 94%</option>
             <option value="/data/galaxy/data/rdp">RDP Trained Set</option>
           </param>
           <param name="dbsize" type="select" label="mer size">
             <option value="5">5</option>
             <option value="6">6</option>
             <option value="7">7</option>
             <option value="8">8</option>
           </param>
         </when>
     </conditional>
     <param name="lambda" type="integer" size="6" value="10000"
label="lambda" help="default 10000"/>
   </inputs>
   <outputs>
     <data name="output" format="tabular" />
   </outputs>
   <help>
   </help>
</tool>



___________________________________________________________
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/



___________________________________________________________
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 | Threaded
Open this post in threaded view
|

Re: Tool Errors

Björn Grüning-3
You can check the stderr and stdout in the information (small i Icon)
site on every dataset. Also can you see what the log is saying? It
should provide you the actuall commandline call, which is produced by
the wrapper.

Cheers,
Bjoern

Am 12.09.2014 um 16:33 schrieb Calvin Morrison:

> Which me thinks is weird, because my code, when given the -v flag will at
> least put out some info to stdout, or worse case, some errors to stderr,
> but those are empty too!
>
> On 12 September 2014 10:31, Björn Grüning <[hidden email]> wrote:
>
>> Hi,
>>
>> as far as I know, it just means your tool did not produced any output, so
>> your results is empty. Nothing more. This is no error, or? The box is not
>> red?
>>
>> Cheers,
>> Bjoern
>>
>> Am 12.09.2014 um 16:28 schrieb Calvin Morrison:
>>
>>> Hi guys,
>>>
>>> I am trying to write a tool with a conditional and for whatever reason the
>>> results, well aren't any results. It just says 'no seek', which totally
>>> bewildering. Does anyone know what this means?
>>>
>>> Thank you,
>>> Calvin
>>>
>>> my xml file:
>>>
>>> <tool id="quikr" name="Quikr">
>>>     <description>Classify with Quikr</description>
>>>     <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>
>>>     <inputs>
>>>       <param name="input" type="data" format="fasta" label="input fasta
>>> file"/>
>>>       <conditional name="qdb">
>>>           <param name="dbtype" type="select" label="Genomes to score
>>> against">
>>>             <option value="default" selected="true">Pretrained
>>> databases</option>
>>>             <option value="user">Custom trained quikr database</option>
>>>           </param>
>>>           <when value="user">
>>>             <param name="dbname" type="data" format="quikrdb" label="custom
>>> trained database"/>
>>>             <param name="dbsize" type="hidden" label="mer size">
>>>               <option value="5">5</option>
>>>             </param>
>>>           </when>
>>>           <when value="default">
>>>             <param name="dbname" type="select" label="Choose database">
>>>               <option value="/data/galaxy/data/gg91">Green Genes
>>> 91%</option>
>>>               <option value="/data/galaxy/data/gg94">Green Genes
>>> 94%</option>
>>>               <option value="/data/galaxy/data/rdp">RDP Trained
>>> Set</option>
>>>             </param>
>>>             <param name="dbsize" type="select" label="mer size">
>>>               <option value="5">5</option>
>>>               <option value="6">6</option>
>>>               <option value="7">7</option>
>>>               <option value="8">8</option>
>>>             </param>
>>>           </when>
>>>       </conditional>
>>>       <param name="lambda" type="integer" size="6" value="10000"
>>> label="lambda" help="default 10000"/>
>>>     </inputs>
>>>     <outputs>
>>>       <data name="output" format="tabular" />
>>>     </outputs>
>>>     <help>
>>>     </help>
>>> </tool>
>>>
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>>>
>>>
>
___________________________________________________________
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 | Threaded
Open this post in threaded view
|

Re: Tool Errors

Calvin Morrison
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.



On 12 September 2014 10:37, Björn Grüning <[hidden email]> wrote:
You can check the stderr and stdout in the information (small i Icon) site on every dataset. Also can you see what the log is saying? It should provide you the actuall commandline call, which is produced by the wrapper.

Cheers,
Bjoern

Am 12.09.2014 um 16:33 schrieb Calvin Morrison:

Which me thinks is weird, because my code, when given the -v flag will at
least put out some info to stdout, or worse case, some errors to stderr,
but those are empty too!

On 12 September 2014 10:31, Björn Grüning <[hidden email]> wrote:

Hi,

as far as I know, it just means your tool did not produced any output, so
your results is empty. Nothing more. This is no error, or? The box is not
red?

Cheers,
Bjoern

Am 12.09.2014 um 16:28 schrieb Calvin Morrison:

Hi guys,

I am trying to write a tool with a conditional and for whatever reason the
results, well aren't any results. It just says 'no seek', which totally
bewildering. Does anyone know what this means?

Thank you,
Calvin

my xml file:

<tool id="quikr" name="Quikr">
    <description>Classify with Quikr</description>
    <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>
    <inputs>
      <param name="input" type="data" format="fasta" label="input fasta
file"/>
      <conditional name="qdb">
          <param name="dbtype" type="select" label="Genomes to score
against">
            <option value="default" selected="true">Pretrained
databases</option>
            <option value="user">Custom trained quikr database</option>
          </param>
          <when value="user">
            <param name="dbname" type="data" format="quikrdb" label="custom
trained database"/>
            <param name="dbsize" type="hidden" label="mer size">
              <option value="5">5</option>
            </param>
          </when>
          <when value="default">
            <param name="dbname" type="select" label="Choose database">
              <option value="/data/galaxy/data/gg91">Green Genes
91%</option>
              <option value="/data/galaxy/data/gg94">Green Genes
94%</option>
              <option value="/data/galaxy/data/rdp">RDP Trained
Set</option>
            </param>
            <param name="dbsize" type="select" label="mer size">
              <option value="5">5</option>
              <option value="6">6</option>
              <option value="7">7</option>
              <option value="8">8</option>
            </param>
          </when>
      </conditional>
      <param name="lambda" type="integer" size="6" value="10000"
label="lambda" help="default 10000"/>
    </inputs>
    <outputs>
      <data name="output" format="tabular" />
    </outputs>
    <help>
    </help>
</tool>



___________________________________________________________
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/





___________________________________________________________
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 | Threaded
Open this post in threaded view
|

Re: Tool Errors

Hans-Rudolf Hotz


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 | Threaded
Open this post in threaded view
|

Re: Tool Errors

Peter Cock
In reply to this post by Calvin Morrison
On Fri, Sep 12, 2014 at 4:11 PM, Calvin Morrison <[hidden email]> 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.

It does help - that command isn't going to work at the shell - try it and see?

The problem is your Cheetah if statement has not been processed,
and I think it is as simple as you've used invalid syntax in your
<command> tag. I think you need to remove the extra spaces to have:

#if ...

Not:

# if ...

Then it might work?

Peter
___________________________________________________________
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 | Threaded
Open this post in threaded view
|

Re: Tool Errors

Calvin Morrison
Yes, it seems that has solved the problem!

I knew it was something silly.

thank you all

On 12 September 2014 11:37, Peter Cock <[hidden email]> wrote:
On Fri, Sep 12, 2014 at 4:11 PM, Calvin Morrison <[hidden email]> 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.

It does help - that command isn't going to work at the shell - try it and see?

The problem is your Cheetah if statement has not been processed,
and I think it is as simple as you've used invalid syntax in your
<command> tag. I think you need to remove the extra spaces to have:

#if ...

Not:

# if ...

Then it might work?

Peter


___________________________________________________________
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/