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 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/

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 bcrain@completegenomics.commailto:bcrain@completegenomics.com

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

Hi Brian,

A couple of days ago, smcmanushttps://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.commailto: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<http://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.jobshttp://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<http://tool.name>} on ${on_string}: coord-sorted read alignments" from_work_dir="alignment/alignment.coordSorted.bam"/>
  <!--        <data format="bam" name="nameSortedBam" label="${tool.name<http://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.

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 bcrain@completegenomics.commailto:bcrain@completegenomics.com

From: John Patterson <jmpatt4@g.uky.edumailto:jmpatt4@g.uky.edu> Date: Thursday, August 16, 2012 12:29 PM To: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto: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 bcrain@completegenomics.commailto:bcrain@completegenomics.com

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

Hi Brian,

A couple of days ago, smcmanushttps://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.commailto: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<http://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.jobshttp://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/~bhaashttp://broad.mit.edu/%7Ebhaas

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

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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.

Thanks, greatly appreciated!

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

From: Scott McManus <scottmcmanus@gatech.edumailto:scottmcmanus@gatech.edu> Date: Friday, August 17, 2012 11:02 AM To: Birgit Crain <bcrain@completegenomics.commailto:bcrain@completegenomics.com> Cc: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] code example for improved error handling

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

-Scott

________________________________ 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 bcrain@completegenomics.commailto:bcrain@completegenomics.com

From: John Patterson <jmpatt4@g.uky.edumailto:jmpatt4@g.uky.edu> Date: Thursday, August 16, 2012 12:29 PM To: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto: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 bcrain@completegenomics.commailto:bcrain@completegenomics.com

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

Hi Brian,

A couple of days ago, smcmanushttps://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.commailto: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<http://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.jobshttp://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/~bhaashttp://broad.mit.edu/%7Ebhaas

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

________________________________

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 see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax . There is a section for "<stdio>, <regex>, and <exit_code> tag sets". The documentation applies to the latest galaxy-dist, though most of what's mentioned (aside from updating stdout and stderr with warning messages) is supported in galaxy-central.

(You can also use the fairly ugly URL http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cstdio.3E.2C... ).

-Scott

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

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 bcrain@completegenomics.com

From: Nicole Rockweiler < n.rockweiler@gmail.com > Date: Friday, July 20, 2012 10:53 AM To: Brian Haas < bhaas@broadinstitute.org > Cc: " galaxy-dev@bx.psu.edu " < galaxy-dev@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-...

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>&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/