Brian;

> I wrote a pipeline (xml attached) that, from what I can gather,
> succeeds, but galaxy shows it as an error and doesn't make the output
> file accessible as a new data set.

Is it possible the software is writing to standard error? Galaxy doesn't
check status codes, but rather check for stderr and assumes that output
indicates a problem. You can wrap the problematic programs with a little
script to eat up stderr and check that everything is okay:

http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr

Brad


>
>>From the server log, I can see that the command line is being
> constructed correctly, and it even indicates that it's captured the
> output, but in the display of the web browser, it just shows up in the
> error state.   The script being run exits (0) on success.  Any ideas?
>
> Here's what the output section of my xml file looks like:
>
> <outputs>
>         <data format="bam" name="coordSortedBam" label="${tool.name}
> on ${on_string}: coord-sorted read alignments"
> from_work_dir="alignment/alignment.coordSorted.bam"/>
> </outputs>
>
> and here's what the server log states:
>
> galaxy.jobs.handler INFO 2012-07-20 09:52:05,240 (30) Job dispatched
> galaxy.jobs.runners.local DEBUG 2012-07-20 09:52:05,453 executing:
> alignReads.pl --target
> /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_26.dat
> -o alignment --aligner bowtie --single
> /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_23.dat
>   --seqType fq
>
> galaxy.jobs DEBUG 2012-07-20 09:52:16,673 finish(): Moved
> /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/job_working_directory/000/30/alignment/alignment.coordSorted.bam
> to /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_50.dat
> as directed by from_work_dir
>
> Again, as far as I can tell, everything worked - but the browser
> doesn't think so.
>
> I've run the exact command above on the command-line, and it exits(0)
> indicating success.
> Also, I've verified that when run through my galaxy instance, the
> galaxy-relocated output file is as expected.
>
> Many thanks for your help.   I'm still getting my feet wet with
> galaxy, reading through all the documentation and searching the
> mailing list for additional help.
>
> best regards,
>
> -brian
>
>
> -- 
> --
> Brian J. Haas
> Manager, Genome Annotation and Analysis, Research and Development
> The Broad Institute
> http://broad.mit.edu/~bhaas
> <tool id="alignreads" name="alignReads" version="0.0.1">
>
>     <description>alignReads: short read alignment tool wrapper</description>
>     <requirements>
>         <requirement type="package">trinity</requirement>
>     </requirements>
>     <command>
>
>         alignReads.pl --target $target -o alignment --aligner 
> $aligner_selection.aligner
>
>
>         ## Inputs.
>         #if str($inputs.paired_or_single) == "paired":
>             --left $inputs.left_input --right $inputs.right_input
>             #if  $inputs.left_input.ext == 'fa':
>                 --seqType fa
>             #else:
>                 --seqType fq
>             #end if
>             #if str($inputs.library_type) != "None":
>                 --SS_lib_type $inputs.library_type
>             #end if
>                       --max_dist_between_pairs $inputs.max_dist_between_pairs
>         #else:
>             --single $inputs.input
>             #if  str($inputs.input.ext) == 'fa':
>                 --seqType fa
>             #else:
>                 --seqType fq
>             #end if
>             #if str($inputs.library_type) != "None":
>                 --SS_lib_type $inputs.library_type
>             #end if
>         #end if
>
>         ## Additional parameters.
>           ##if str($inputs.use_additional) == "yes":
>               ##      -- $inputs.additional_params
>         ##end if
>       
>                 
>         ## direct to output
>           ##    > $trinity_log 2>&amp;1
>  
>
>
>     </command>
>     <inputs>
>               <param format="fasta" name="target" type="data" label="target" 
> help="Fasta sequences targeted for short-read alignment"  />
>
>         <conditional name="inputs">
>                   <param name="paired_or_single" type="select" label="Paired 
> or Single-end data?">
>                 <option value="paired">Paired</option>
>                 <option value="single">Single</option>
>             </param>
>             <when value="paired">
>                 <param format="fasta,fastq" name="left_input" type="data" 
> label="Left/Forward strand reads" help=""/>
>                 <param format="fasta,fastq" name="right_input" type="data" 
> label="Right/Reverse strand reads" help=""/>
>                 <param name="library_type" type="select" 
> label="Strand-specific Library Type">
>                     <option value="None">None</option>
>                     <option value="FR">FR</option>
>                     <option value="RF">RF</option>
>                 </param>
>                 <param name="max_dist_between_pairs" type="integer" 
> value="2000" min="1" label="max_dist_between_pairs" help="Maximum length 
> expected between fragment pairs as aligned to the target, including introns 
> where relevant."/>
>
>
>             </when>
>             <when value="single">
>                 <param format="fasta,fastq" name="input" type="data" 
> label="Single-end reads" help=""/>
>                 <param name="library_type" type="select" 
> label="Strand-specific Library Type">
>                     <option value="None">None</option>
>                     <option value="F">F</option>
>                     <option value="R">R</option>
>                 </param>
>             </when>
>         </conditional>
>
>               <conditional name="aligner_selection">
>                       <param name="aligner" type="select" label="Select 
> alignment tool to run">
>                               <option value="bowtie">bowtie</option>
>                               <option value="bwa">bwa</option>
>                               <option value="blat">blat</option>
>                       </param>
>                       <when value="blat">
>                               <param name="max_intron_length" type="integer" 
> value="10000" min = "1" label="maximum intron length" help="" />
>                               <param name="min_percent_identity" 
> type="integer" value="95" min="1" label="minimum percent identity" help="" />
>                       </when>
>                       <when value="bwa">
>                       </when>
>                       <when value="bowtie">
>                       </when>
>               </conditional>
>
>
>       <!--            
>               <conditional name="use_additional_params">
>             <param name="use_additional" type="select" label="Use Additional 
> Params?">
>                 <option value="no">No</option>
>                 <option value="yes">Yes</option>
>             </param>
>             <when value="no">
>             </when>
>             <when value="yes">            
>                               <param name="additional_params" type="text" 
> value="" label="Additional command-line parameters to aligner" help="" />
>             </when>
>         </conditional>
>     
>       -->
>
>     </inputs>
>     <outputs>
>         <data format="bam" name="coordSortedBam" label="${tool.name} on 
> ${on_string}: coord-sorted read alignments" 
> from_work_dir="alignment/alignment.coordSorted.bam"/>
>       <!--        <data format="bam" name="nameSortedBam" label="${tool.name} 
> on ${on_string}: name-sorted read alignments" 
> from_work_dir="alignment/alignment.nameSorted.bam"/> -->
>       </outputs>
>     <tests>
>     </tests>
>     <help>
>         .. _Trinity: http://trinityrnaseq.sourceforge.net
>     </help>
> </tool>
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