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-...
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 toolwrapper</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="Selectalignment 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="UseAdditional 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:
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