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Pasquale Notarangelo
Hi all,
we are two new galaxy users.

We have developed 2 new tools and we would connect them into a new
workflow.

We are able to import both tools and to link them into a workflow but we
aren't able to pass the output of the first tool as the input of the
second tool.


The first tool calls a bash script that produces a simple string (this
is the path of the file generated by the script).

This is the xnl file of the first tool:

<tool id="infnTools_ConcatenateArgumentsTool" name="Concatenate
Arguments and generate file Tool">

   <description>Concatenate arguments strings and generate
file</description>

   <command interpreter="bash">concatenateArgumentsAndPutFile.sh
$inputArguments</command>

   <inputs>
     <param name="inputArguments" type="text" label="ARGUMENTS"
optional="false"/>
   </inputs>

   <outputs>
     <data format="string" name="output" />
   </outputs>

</tool>


This is the bash script of the first tool
(concatenateArgumentsAndPutFile.sh):

#!/bin/bash
echo "ARGUMENTS:" $@
export PathFile=/tmp/$RANDOM$RANDOM
echo $@ > $PathFile
echo "PathFile:" $PathFile


The xml of the second tool is the following:

<tool id="infnTools_InsertBiomasTools" name="InsertJobs and check the
status of Biomas">
   <description>InsertJobs Biomas Tool and check the status</description>

   <command interpreter="bash">insertAndCheckBiomasJobs.sh  $input
</command>

   <inputs>
        <param format="string" name="input" type="data" label="Insert path
file"/>
   </inputs>

   <outputs>
     <data format="tabular" name="output"/>
   </outputs>

</tool>


When we run the workflow the output of the first tool isn't seen as
input of the second tool.

Into the galaxy history we see this value for the input of the second
tool: /home/pasquale/galaxy-dist/database/files/000/dataset_83.dat

Also this file is emtpy.


How we can resolve the problem?

Thanks and best regard
Pasquale & Alfonso


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Dott. Pasquale Notarangelo
INFN Istituto Nazionale di Fisica Nucleare - Sezione Bari

Via Orabona, 4 - 70126 Bari, Italy

Tel. ufficio: +39 080-5443194
Interno ufficio: 3194
Mail: [hidden email]
Skype: pasquale.notarangelo_1985
Msn: [hidden email]
Gmail: [hidden email]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
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use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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Re: Help

Jen Hillman-Jackson
Hi Pasquale,

 From a quick look (and I am not the tool-building expert of our team!),
I suspect that the problem is with the "format" assigned to the output
of the first tool, and input of the second tool. Specifically,
"format=string" is problematic, unless you have also defined this in
your local install. Even then, having it contain a path to a file
deviates from the regular usage (if I have understood your snippet of
code correctly).

Our wiki for tool configuration is located here. The wiki has examples,
but you can also look at tools in the source code or Tool shed repos to
see how "format" is used.
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

I don't want to send you away from this list, since I know that you
already emailed earlier, but the [hidden email] mailing list is
where most tool development questions are discussed. That said, when
troubleshooting, individual scripts are not often corrected by the
community if the answer is already in the wiki, existing code base, or
in a prior discussion. So, making use of these resources is the first
place to start. There is a search tool for development topics that can
be of great use to locate the bits for you that can be helpful:
http://galaxyproject.org/search/

Try a search with "Admin & Development" - I found in the first few hits
this link, which includes the tool config link above plus many other
related resources listed at the bottom:
https://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial

Hopefully this helps a little, and others reading the post are welcome
to add in more of course!

Jen
Galaxy team

On 1/13/14 7:31 AM, Pasquale Notarangelo wrote:

> Hi all,
> we are two new galaxy users.
>
> We have developed 2 new tools and we would connect them into a new
> workflow.
>
> We are able to import both tools and to link them into a workflow but
> we aren't able to pass the output of the first tool as the input of
> the second tool.
>
>
> The first tool calls a bash script that produces a simple string (this
> is the path of the file generated by the script).
>
> This is the xnl file of the first tool:
>
> <tool id="infnTools_ConcatenateArgumentsTool" name="Concatenate
> Arguments and generate file Tool">
>
>   <description>Concatenate arguments strings and generate
> file</description>
>
>   <command interpreter="bash">concatenateArgumentsAndPutFile.sh
> $inputArguments</command>
>
>   <inputs>
>     <param name="inputArguments" type="text" label="ARGUMENTS"
> optional="false"/>
>   </inputs>
>
>   <outputs>
>     <data format="string" name="output" />
>   </outputs>
>
> </tool>
>
>
> This is the bash script of the first tool
> (concatenateArgumentsAndPutFile.sh):
>
> #!/bin/bash
> echo "ARGUMENTS:" $@
> export PathFile=/tmp/$RANDOM$RANDOM
> echo $@ > $PathFile
> echo "PathFile:" $PathFile
>
>
> The xml of the second tool is the following:
>
> <tool id="infnTools_InsertBiomasTools" name="InsertJobs and check the
> status of Biomas">
>   <description>InsertJobs Biomas Tool and check the status</description>
>
>   <command interpreter="bash">insertAndCheckBiomasJobs.sh $input
> </command>
>
>   <inputs>
>     <param format="string" name="input" type="data" label="Insert path
> file"/>
>   </inputs>
>
>   <outputs>
>     <data format="tabular" name="output"/>
>   </outputs>
>
> </tool>
>
>
> When we run the workflow the output of the first tool isn't seen as
> input of the second tool.
>
> Into the galaxy history we see this value for the input of the second
> tool: /home/pasquale/galaxy-dist/database/files/000/dataset_83.dat
>
> Also this file is emtpy.
>
>
> How we can resolve the problem?
>
> Thanks and best regard
> Pasquale & Alfonso
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Dott. Pasquale Notarangelo
> INFN Istituto Nazionale di Fisica Nucleare - Sezione Bari
>
> Via Orabona, 4 - 70126 Bari, Italy
>
> Tel. ufficio: +39 080-5443194
> Interno ufficio: 3194
> Mail: [hidden email]
> Skype: pasquale.notarangelo_1985
> Msn: [hidden email]
> Gmail: [hidden email]
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> 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/

--
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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/
Jennifer Hillman-Jackson
http://galaxyproject.org