[galaxy-dev] Could anyone body tell me why our C program do not work in galaxy

Dannon Baker dannonbaker at me.com
Fri Apr 22 10:32:00 EDT 2011


Without seeing an error message I'll guess that issue is that there is no C interpreter.  Your program is a compiled executable.

Try the following and let me know (including any error messages) if it doesn't work:

<command>
  shortest_path  $infile1  $output
</command>

-Dannon


On Apr 22, 2011, at 2:12 AM, liyanhui607 wrote:

> Dear Sir,
>           We have a program writen in C lanuage. It can run nomally in linux environment.
>            We plan to add it to galaxy, but it did not work.
>            The C file after complie named "shortest-path"
>              The shortest-path.xml is as follow:
>           Could anybody tell me what is wrong ? why it does not work?
>            Thank you very much!
>  
> Best Wishes!
>  
> Yan-Hui Li
>  
>  
>              <tool id="shortest_path_1" name="shortest_path">
>          <command interpreter="C">./shortest_path  $infile1  $output </command>
>         <inputs>
>                 <param format="text" name="infile1" type="data"
>                         label="
> expressed_genes_20101024.hprd8_biogrid-2.0.58.adj_matrix.txt
>                         "/>
>         </inputs>
>         <outputs>
>                 <data format="tabular" name="output" />
>         </outputs>
>         <tests>
>                 <test>
>                         <param name="input" value="1"/>
>                         <param name="input" value="../GEO_dataset/expressed_genes_u133a.6k_u133p2.8k_20101024.txt"/>
>                         <param name="input" value="../ppi/hprd8_biogrid-2.0.58.ppi.txt"/>
>                         <output name="out_file1" file="expressed_genes_20101024.hprd8_biogrid-2.0.58.ppi.txt"/>
>                 </test>
>         </tests>
> </tool>
> 
> 
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