Hi Brian, A couple of days ago, smcmanus <https://bitbucket.org/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>&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
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