I'm writing documentation now - I'll have something this afternoon. 
Sorry for the delay. 

-Scott 

----- Original Message -----

> No, I call the executable directly from the xml. It kept failing
> although it seemed to finish the job and I realized that on success
> the executable prints a summary message to stderror, because it's
> using stdout for the actual results so they can be pipped to another
> command.
> From the July news brief I understood that you can now add code to
> the xml to check the stdout and std error for messages and I was
> wondering if you have any documentation or sample code for that in
> any published tool.

> Thanks

> Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete
> Genomics, Inc.
> (650) 428-6023 office | (408) 605-3938 mobile
> bcr...@completegenomics.com

> From: John Patterson < jmpa...@g.uky.edu >
> Date: Thursday, August 16, 2012 12:29 PM
> To: " galaxy-dev@lists.bx.psu.edu " < galaxy-dev@lists.bx.psu.edu >
> Subject: Re: [galaxy-dev] code example for improved error handling

> On 08/16/2012 03:02 PM, Birgit Crain wrote:

> > Hi
> 

> > I'm writing a tools for an executable that writes results to stdout
> > and reports success message to stderr, so it really need the
> > improved error handling. Is there any sample code or documentation
> > available?
> 

> > Thanks
> 

> > Birgit Crain, Ph.D. | Sr. Professional Services Scientist |
> > Complete
> > Genomics, Inc.
> 
> > (650) 428-6023 office | (408) 605-3938 mobile
> 
> > bcr...@completegenomics.com
> 

> > From: Nicole Rockweiler < n.rockwei...@gmail.com >
> 
> > Date: Friday, July 20, 2012 10:53 AM
> 
> > To: Brian Haas < bh...@broadinstitute.org >
> 
> > Cc: " galaxy-...@bx.psu.edu " < galaxy-...@bx.psu.edu >
> 
> > Subject: Re: [galaxy-dev] pipeline execution succeeds but galaxy
> > shows failure
> 

> > 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
> 

> > The contents of this e-mail and any attachments are confidential
> > and
> > only for use by the intended recipient. Any unauthorized use,
> > distribution or copying of this message is strictly prohibited. If
> > you are not the intended recipient please inform the sender
> > immediately by reply e-mail and delete this message from your
> > system. Thank you for your co-operation.
> 

> > ___________________________________________________________
> 
> > 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/
> 
> Hi

> Let me get this straight first. Are you writing python scripts that
> pass commands to this executable? If so, you are doing something
> similar to my tool. In this case, all prints to stderr will cause
> galaxy to report a failed run even if the run is successful.

> Set up the command and then make a sub process call with try/except:
> Need to import errno.

> try:
> retcode = subprocess.call(dividereads_cmd, stderr=subprocess.STDOUT,
> stdout=splice_log)
> except OSError, o:
> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:
> print >> sys.stdout, fail_str, "Error: /insert name here/ not found
> on this system"
> exit(1)

> Here is some documentation on errno:
> http://docs.python.org/library/errno.html

> The important thing is to redirect the stderr from the executable
> with the subprocess call. I'd suggest printing your success messages
> and or debugging to a log file.

> -John

> The contents of this e-mail and any attachments are confidential and
> only for use by the intended recipient. Any unauthorized use,
> distribution or copying of this message is strictly prohibited. If
> you are not the intended recipient please inform the sender
> immediately by reply e-mail and delete this message from your
> system. Thank you for your co-operation.
> ___________________________________________________________
> 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/
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