[Bioperl-l] Re: [Bioperl-pipeline] biopipe/Pipeline Manager

[Shawn Hoon]

Its relatively easy to have multiple inputs.
Have all your input files in one directory.

In the xml,
change the input_file parameter to input_dir:

like so
:
<pipeline_setup>
     <global
           rootdir="t/"
           datadir="$rootdir/data"
           resultdir="$datadir/phylip_result"
           workdir="$datadir/phylip_dir"
           inputdir="$datadir/phylip_in"
           msa_logicname="Clustalw"
           msa_program= "clustalw"
           msa_param = "-ktuple 2 -matrix BLOSUM"
     />


   <pipeline_flow_setup>
     <analysis id="1">
       <data_monger>
         <initial/>
         <input>
           <name>input_dir</name>
         </input>
         <input_create>
            <module>setup_file</module>
            <rank>1</rank>
            <argument>
              <tag>tag</tag>
              <value>infile</value>
            </argument>
             <argument>
                 <tag>input_dir</tag>
                 <value>$inputdir</value>
                 <type>SCALAR</type>
             </argument>
             <argument>

So what this will do will be to create a job one for each input file.  
Each file will should contain the multi-fasta files.
Let me know if this works for you.

hth,

shawn


On Monday, December 15, 2003, at 12:25AM, matthieu CONTE wrote:

>
> Hello,
> I  working on Biopipe by using Pipeline Manager. I work with modified  
> version of "phylip_tree_pipeline.xml"
> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-pipeline/ 
> xml/examples/xml/phylip_tree_pipeline.xml?cvsroot=bioperl
>
> My problem is that I do not have only one input file but 1128   
> differents files in input !
>
> My input files are multifasta with a set of protein from Arabidopsis  
> thaliana and Oryza sativa
> containing a specific PFAM motif.
> The path for example for the motif PF00012 is:   
> /PF00012/fasta_PF00012/PF00012.fa and so on for the 1128 motifs.
>
> What I want to do is to loop on the 1128 PFAM files.
>
> Enter the PFAM number in a let's say $pf
>
> Start the job with the Path /$pf/fasta_$pf/$pf.fa file
>
> But I don't find any way to work with a non global variable
> Does somebody have an idea?
> Is it possible to modify Pipeline Manager so that it can hang argument  
> an input file?
>
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