Hi Brian,

A couple of days ago, smcmanus pushed the following change to the repo:

Tools can now specify their own handling of stderr and stdout regular expressions as well as exit code ranges.

https://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-decide-whether-to-use-return-codes-or-stderr-for-detecting-job

It looks like the documentation has yet to be written.

Hope this helps,

Nicole

On Fri, Jul 20, 2012 at 12:46 PM, Brad Chapman <chapmanb@50mail.com> wrote:

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>&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>
>
>
> 
>
> </inputs>

> <outputs>
> <data format="bam" name="coordSortedBam" label="${tool.name} on ${on_string}: coord-sorted read alignments" from_work_dir="alignment/alignment.coordSorted.bam"/>

> 
> </outputs>
> <tests>
> </tests>
> <help>
> .. _Trinity: http://trinityrnaseq.sourceforge.net
> </help>
> </tool>
> ___________________________________________________________
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___________________________________________________________
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--
Nicole Rockweiler
Genome Technology Access Center
Washington University in St. Louis
Campus Box 8510
4444 Forest Park Avenue
Saint Louis, MO 63108