Thanks Brad and Nicole!   This definitely explains it.  The stderr
(which almost all my tools generate for monitoring purposes) was
resulting in galaxy thinking the process failed.

All is well and good now.  HUGE THANKS!!!!!


-brian


On Fri, Jul 20, 2012 at 1:53 PM, Nicole Rockweiler
<n.rockwei...@gmail.com> wrote:
> 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 <chapm...@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>&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>
>> > ___________________________________________________________
>> > Please keep all replies on the list by using "reply all"
>> > in your mail client.  To manage your subscriptions to this
>> > and other Galaxy lists, please use the interface at:
>> >
>> >   http://lists.bx.psu.edu/
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>
>
>
>
> --
> Nicole Rockweiler
> Genome Technology Access Center
> Washington University in St. Louis
> Campus Box 8510
> 4444 Forest Park Avenue
> Saint Louis, MO 63108



-- 
--
Brian J. Haas
Manager, Genome Annotation and Analysis, Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas
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