new tool works correctly but galaxy thinks it failed

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new tool works correctly but galaxy thinks it failed

ryang
 Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed.  I checked the output file the tools create, and it succeeded. 

How do I tell Galaxy that a tool it ran was successful?  Is it something in my XML file?  The tool is outputting some info to stderr.  Could this be why?

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Re: new tool works correctly but galaxy thinks it failed

Dannon Baker-2
Hey Ryan,

Yes, this is exactly why.  By default, galaxy expects that anything written to stderr means that there was a failure, though you can change this by using the error_code syntax (among other options) found here:  https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

-Dannon

On Tue, Apr 28, 2015 at 11:41 AM Ryan G <[hidden email]> wrote:
 Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed.  I checked the output file the tools create, and it succeeded. 

How do I tell Galaxy that a tool it ran was successful?  Is it something in my XML file?  The tool is outputting some info to stderr.  Could this be why?
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Re: new tool works correctly but galaxy thinks it failed

Peter Cock
In reply to this post by ryang
You probably need to set the <stdio> tag, since due to a
historical design choice by default any output on stderr
is treated as an error. See:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

Peter

On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <[hidden email]> wrote:

>  Hi - I implemented a tool I us into Galaxy but when I run the tool view
> Galaxy, Galaxy thinks the tool failed.  I checked the output file the tools
> create, and it succeeded.
>
> How do I tell Galaxy that a tool it ran was successful?  Is it something in
> my XML file?  The tool is outputting some info to stderr.  Could this be
> why?
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: new tool works correctly but galaxy thinks it failed

ryang
ok, thanks.  Let me look at this.  When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly.


On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <[hidden email]> wrote:
You probably need to set the <stdio> tag, since due to a
historical design choice by default any output on stderr
is treated as an error. See:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

Peter

On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <[hidden email]> wrote:
>  Hi - I implemented a tool I us into Galaxy but when I run the tool view
> Galaxy, Galaxy thinks the tool failed.  I checked the output file the tools
> create, and it succeeded.
>
> How do I tell Galaxy that a tool it ran was successful?  Is it something in
> my XML file?  The tool is outputting some info to stderr.  Could this be
> why?
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/


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Re: new tool works correctly but galaxy thinks it failed

Dannon Baker-2
Like Peter mentions, we did this because historically not all tools used (still don't, I guess) exit codes correctly.  If yours does, you can set exit_code tags and everything should work.

On Tue, Apr 28, 2015 at 11:47 AM Ryan G <[hidden email]> wrote:
ok, thanks.  Let me look at this.  When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly.


On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <[hidden email]> wrote:
You probably need to set the <stdio> tag, since due to a
historical design choice by default any output on stderr
is treated as an error. See:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

Peter

On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <[hidden email]> wrote:
>  Hi - I implemented a tool I us into Galaxy but when I run the tool view
> Galaxy, Galaxy thinks the tool failed.  I checked the output file the tools
> create, and it succeeded.
>
> How do I tell Galaxy that a tool it ran was successful?  Is it something in
> my XML file?  The tool is outputting some info to stderr.  Could this be
> why?
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

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Re: new tool works correctly but galaxy thinks it failed

ryang
  <stdio>
    <exit_code range="-1" level="fatal" description="RandomSubFq failed" />
  </stdio>


this works.  Thanks.

On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker <[hidden email]> wrote:
Like Peter mentions, we did this because historically not all tools used (still don't, I guess) exit codes correctly.  If yours does, you can set exit_code tags and everything should work.

On Tue, Apr 28, 2015 at 11:47 AM Ryan G <[hidden email]> wrote:
ok, thanks.  Let me look at this.  When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly.


On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <[hidden email]> wrote:
You probably need to set the <stdio> tag, since due to a
historical design choice by default any output on stderr
is treated as an error. See:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

Peter

On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <[hidden email]> wrote:
>  Hi - I implemented a tool I us into Galaxy but when I run the tool view
> Galaxy, Galaxy thinks the tool failed.  I checked the output file the tools
> create, and it succeeded.
>
> How do I tell Galaxy that a tool it ran was successful?  Is it something in
> my XML file?  The tool is outputting some info to stderr.  Could this be
> why?
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: new tool works correctly but galaxy thinks it failed

John Chilton-4
I feel like that stdio tag is going to cause it to always pass - even
if the exit code is not 0. Am I wrong? I like:

    <stdio>
        <exit_code range="1:" />
    </stdio>

myself. Björn Grüning uses -

<stdio>
<exit_code range="1:" />
<exit_code range=":-1" />
<regex match="Error:" />
<regex match="Exception:" />
</stdio>

which is a popular choice.

As a heads up for people reading discussion in the future - starting
in 15.05 - you will be able to just add detect_errors="exit_code" on
the command tag to get a more sensible default behavior.
https://github.com/galaxyproject/galaxy/pull/117

-John


On Tue, Apr 28, 2015 at 12:12 PM, Ryan G <[hidden email]> wrote:

>   <stdio>
>     <exit_code range="-1" level="fatal" description="RandomSubFq failed" />
>   </stdio>
>
>
> this works.  Thanks.
>
> On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker <[hidden email]>
> wrote:
>>
>> Like Peter mentions, we did this because historically not all tools used
>> (still don't, I guess) exit codes correctly.  If yours does, you can set
>> exit_code tags and everything should work.
>>
>> On Tue, Apr 28, 2015 at 11:47 AM Ryan G <[hidden email]>
>> wrote:
>>>
>>> ok, thanks.  Let me look at this.  When I look at the information about
>>> the tool, Galaxy does see the exit code is 0, which I think would be
>>> sufficient to know the tool ran correctly.
>>>
>>>
>>> On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <[hidden email]>
>>> wrote:
>>>>
>>>> You probably need to set the <stdio> tag, since due to a
>>>> historical design choice by default any output on stderr
>>>> is treated as an error. See:
>>>>
>>>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
>>>>
>>>> Peter
>>>>
>>>> On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <[hidden email]>
>>>> wrote:
>>>> >  Hi - I implemented a tool I us into Galaxy but when I run the tool
>>>> > view
>>>> > Galaxy, Galaxy thinks the tool failed.  I checked the output file the
>>>> > tools
>>>> > create, and it succeeded.
>>>> >
>>>> > How do I tell Galaxy that a tool it ran was successful?  Is it
>>>> > something in
>>>> > my XML file?  The tool is outputting some info to stderr.  Could this
>>>> > be
>>>> > why?
>>>> >
>>>> > ___________________________________________________________
>>>> > 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:
>>>> >   https://lists.galaxyproject.org/
>>>> >
>>>> > 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:
>>>   https://lists.galaxyproject.org/
>>>
>>> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: new tool works correctly but galaxy thinks it failed

ryang
You are correct.  It's always passing even when it fails. There was nothing in the docs to indicate a pass.

Sent from my iPhone

> On Apr 28, 2015, at 3:44 PM, John Chilton <[hidden email]> wrote:
>
> I feel like that stdio tag is going to cause it to always pass - even
> if the exit code is not 0. Am I wrong? I like:
>
>  <stdio>
>      <exit_code range="1:" />
>  </stdio>
>
> myself. Björn Grüning uses -
>
> <stdio>
> <exit_code range="1:" />
> <exit_code range=":-1" />
> <regex match="Error:" />
> <regex match="Exception:" />
> </stdio>
>
> which is a popular choice.
>
> As a heads up for people reading discussion in the future - starting
> in 15.05 - you will be able to just add detect_errors="exit_code" on
> the command tag to get a more sensible default behavior.
> https://github.com/galaxyproject/galaxy/pull/117
>
> -John
>
>
>> On Tue, Apr 28, 2015 at 12:12 PM, Ryan G <[hidden email]> wrote:
>> <stdio>
>>  <exit_code range="-1" level="fatal" description="RandomSubFq failed" />
>> </stdio>
>>
>>
>> this works.  Thanks.
>>
>> On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker <[hidden email]>
>> wrote:
>>>
>>> Like Peter mentions, we did this because historically not all tools used
>>> (still don't, I guess) exit codes correctly.  If yours does, you can set
>>> exit_code tags and everything should work.
>>>
>>> On Tue, Apr 28, 2015 at 11:47 AM Ryan G <[hidden email]>
>>> wrote:
>>>>
>>>> ok, thanks.  Let me look at this.  When I look at the information about
>>>> the tool, Galaxy does see the exit code is 0, which I think would be
>>>> sufficient to know the tool ran correctly.
>>>>
>>>>
>>>> On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <[hidden email]>
>>>> wrote:
>>>>>
>>>>> You probably need to set the <stdio> tag, since due to a
>>>>> historical design choice by default any output on stderr
>>>>> is treated as an error. See:
>>>>>
>>>>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
>>>>>
>>>>> Peter
>>>>>
>>>>> On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <[hidden email]>
>>>>> wrote:
>>>>>> Hi - I implemented a tool I us into Galaxy but when I run the tool
>>>>>> view
>>>>>> Galaxy, Galaxy thinks the tool failed.  I checked the output file the
>>>>>> tools
>>>>>> create, and it succeeded.
>>>>>>
>>>>>> How do I tell Galaxy that a tool it ran was successful?  Is it
>>>>>> something in
>>>>>> my XML file?  The tool is outputting some info to stderr.  Could this
>>>>>> be
>>>>>> why?
>>>>>>
>>>>>> ___________________________________________________________
>>>>>> 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:
>>>>>> https://lists.galaxyproject.org/
>>>>>>
>>>>>> 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:
>>>> https://lists.galaxyproject.org/
>>>>
>>>> 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:
>> https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
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dynamic_options within repeat or conditional block

Linda Bakker
Hi All,

I am relatively new to galaxy and recently had to take over the work on
several tools.
After the last galaxy update, one of them stopped working.

Old working code:

        <repeat name="pref" title="Select column name preference">
                 <param name="columntype" type="select" label="Column
name" refresh_on_change="true"
                dynamic_options='filter_column2(library_file, col_type,
polarity)' />
       </repeat>

This worked perfectly, but now, the select shows me "no options available"
When i move the param-tag out of the repeat block, it works again.
Also, when i put this param within a conditional like:

       <conditional name="col_pref">
           <param name="apply_select" type="boolean" checked="false"
label="Select column name preference?" />
           <when value="true">
               <param name="columntype" type="select" label="Column
name" refresh_on_change="true"
dynamic_options='filter_column2(library_file,col_type,polarity)'/>
           </when>
           <when value="false">
             <param name="model" type="hidden" value="False" />
           </when>
       </conditional>

the dynamic_options also does not work.
I found a trello -bug report:
https://trello.com/c/UJKGsWSu/2469-dynamic-options-in-select-fields-do-not-work-in-repeats
This seems to be my problem too.

Can someone confirm for me that it is not possible to use the
dynamic_options from within a repeat or conditional block, or am i
missing something? Otherwise i have to come up with some sort of workaround.

Thank you,

Linda Bakker


--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: [hidden email]

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: dynamic_options within repeat or conditional block

Aysam Guerler
Hey Linda,

This seems to be an issue which has already been fixed. Could you please update your instance and/or let me know at which commit it is?

Thank you,
Aysam

On Thu, Apr 30, 2015 at 6:41 AM, Linda Bakker <[hidden email]> wrote:
Hi All,

I am relatively new to galaxy and recently had to take over the work on several tools.
After the last galaxy update, one of them stopped working.

Old working code:

       <repeat name="pref" title="Select column name preference">
                <param name="columntype" type="select" label="Column name" refresh_on_change="true"
               dynamic_options='filter_column2(library_file, col_type, polarity)' />
      </repeat>

This worked perfectly, but now, the select shows me "no options available"
When i move the param-tag out of the repeat block, it works again.
Also, when i put this param within a conditional like:

      <conditional name="col_pref">
          <param name="apply_select" type="boolean" checked="false" label="Select column name preference?" />
          <when value="true">
              <param name="columntype" type="select" label="Column name" refresh_on_change="true"
dynamic_options='filter_column2(library_file,col_type,polarity)'/>
          </when>
          <when value="false">
            <param name="model" type="hidden" value="False" />
          </when>
      </conditional>

the dynamic_options also does not work.
I found a trello -bug report: https://trello.com/c/UJKGsWSu/2469-dynamic-options-in-select-fields-do-not-work-in-repeats
This seems to be my problem too.

Can someone confirm for me that it is not possible to use the dynamic_options from within a repeat or conditional block, or am i missing something? Otherwise i have to come up with some sort of workaround.

Thank you,

Linda Bakker


--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: <a href="tel:%2B31-317-480756" value="+31317480756" target="_blank">+31-317-480756
email: [hidden email]

___________________________________________________________
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:
 https://lists.galaxyproject.org/

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


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: dynamic_options within repeat or conditional block

Linda Bakker
Thanks for your reply,
I updated my instance and indeed it was fixed!
I will update more frequently!

Linda


On 04/30/2015 03:29 PM, Aysam Guerler wrote:
Hey Linda,

This seems to be an issue which has already been fixed. Could you please update your instance and/or let me know at which commit it is?

Thank you,
Aysam

On Thu, Apr 30, 2015 at 6:41 AM, Linda Bakker <[hidden email]> wrote:
Hi All,

I am relatively new to galaxy and recently had to take over the work on several tools.
After the last galaxy update, one of them stopped working.

Old working code:

       <repeat name="pref" title="Select column name preference">
                <param name="columntype" type="select" label="Column name" refresh_on_change="true"
               dynamic_options='filter_column2(library_file, col_type, polarity)' />
      </repeat>

This worked perfectly, but now, the select shows me "no options available"
When i move the param-tag out of the repeat block, it works again.
Also, when i put this param within a conditional like:

      <conditional name="col_pref">
          <param name="apply_select" type="boolean" checked="false" label="Select column name preference?" />
          <when value="true">
              <param name="columntype" type="select" label="Column name" refresh_on_change="true"
dynamic_options='filter_column2(library_file,col_type,polarity)'/>
          </when>
          <when value="false">
            <param name="model" type="hidden" value="False" />
          </when>
      </conditional>

the dynamic_options also does not work.
I found a trello -bug report: https://trello.com/c/UJKGsWSu/2469-dynamic-options-in-select-fields-do-not-work-in-repeats
This seems to be my problem too.

Can someone confirm for me that it is not possible to use the dynamic_options from within a repeat or conditional block, or am i missing something? Otherwise i have to come up with some sort of workaround.

Thank you,

Linda Bakker


--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: <a moz-do-not-send="true" href="tel:%2B31-317-480756" value="+31317480756" target="_blank">+31-317-480756
email: [hidden email]

___________________________________________________________
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:
 https://lists.galaxyproject.org/

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



-- 
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: [hidden email]

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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