On Wed, Apr 25, 2012 at 11:48 AM, Dan Tenenbaum <dtene...@fhcrc.org> wrote:
> On Wed, Apr 25, 2012 at 9:53 AM, Dan Tenenbaum <dtene...@fhcrc.org> wrote:
>> Hello Hans-Rudolph,
>>
>> On Wed, Apr 25, 2012 at 1:37 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>>> Hi Dan
>>>
>>>
>>> There seems to be several issues connected with each other or not, I don't
>>> know.....
>>>
>>>
>>> - Let's start with the 'curiosity': Do you get this problem with any
>>>  tool?
>>
>> No. And, I should be a bit more specific about what happens. When I
>> click "execute" I see this:
>>
>> The following job has been successfully added to the queue:
>>
>> 36: RNASeq tool on data 3 and data 4
>> 37: RNASeq tool on data 3 and data 4
>>
>>
>> Does it also happen with a 'simple' (ie not using R) tool you
>>>  add?
>>>
>>
>> No.
>>
>>> - When you execute your R script on the command line, are you running
>>>  it as the same user as Galaxy executes the job?
>>
>> Yes.
>>
>>
>>>
>>>
>>> - we execute R scripts the following way:
>>>
>>>  <command>Rscript --vanilla /full path to script/script.R -n $name
>>>     -i $infile -o $outfile</command>
>>>
>>>  and in the R script we use the library 'getopt'
>>>
>>>
>>>
>>
>> Good idea. Taking a closer, look, I found my R script was not
>> expecting arguments in the same order that the XML script provided
>> them in.
>> I fixed that and now the R script runs without warning or error, but I
>> still get the "8-bit bytestrings" error, and the error "Unable to
>> finish job".
>>
>> However, by printing out the arguments within R, I can see the name of
>> the output files that are supposed to be generated, and it looks like
>> they are generated. So why doesn't the job finish?
>>

Sorry for the noise of answering my own question, which I find has
been asked and answered before, but perhaps this will help someone.

Here's the answer:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-August/003161.html

Basically, if any output goes to STDERR, galaxy considers that the job
failed. The link above suggests to do this:

jobcommand ARGS 2>/dev/null

But I changed that to:

jobcommand ARGS 2>&1

that way, STDERR is redirected to STDOUT and any important diagnostic
information originally printed to STDERR is not lost.

I added this to my Rscript_wrapper.sh
script and all is well.

Thanks,
Dan


>> I think the 8 bit bytestrings error might be because R outputs
>> backticks (`) and they show up escaped in the galaxy error like this:
>> \xe2\x80\x98.
>>
>> Is there some way that I can set my LOCALE so that R uses an encoding
>> that galaxy is happier with? Or perhaps I can get R to stop outputting
>> those backticks somehow.
>
> Answering my own question here (but following up with more questions).
> R was ouputting not backticks but curly quotes, and I turned these off
> by putting:
>
> options("useFancyQuotes" = FALSE)
>
> in my R script.
>
> However, my R script is still failing:
>
> Dataset generation errors
>
> Dataset 46: RNASeq tool on data 3 and data 4
>
> Tool execution generated the following error message:
> BiocInstaller version 1.5.7, ?biocLite for help
> Loading required package: org.Dm.eg.db
> Loading required package: AnnotationDbi
> Loading required package: BiocGenerics
>
> Attaching package: 'BiocGenerics'
>
> The following object(s) are masked from 'package:stats':
>
>    xtabs
>
> The following object(s) are masked from 'package:base':
>
>    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
>    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
>    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
>    rownames, sapply, setdiff, table, tapply, union, unique
>
> Loading required package: Biobase
> Welcome to Bioconductor
>
>    Vignettes contain introductory material; view with
>    'browseVignettes()'. To cite Bioconductor, see
>    'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Loading required package: DBI
>
> Calculating library sizes from column totals.
> Running estimateCommonDisp() on DGEList object before proceeding with
> estimateTagwiseDisp().
> The tool produced the following additional output:
> pdf_outfile=
> /Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_46.dat
> csv_outfile=
> /Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_47.dat
> pdf
>  2
>
> The thing is, none of this is an error. This is the exact output the
> script is supposed to produce, and it prints out the filenames of the
> two output files it creates, and I can verify that those exist and
> have the correct contents. So why does it say there is an error?
>
> Could it be the return code?
> I added
> q(save="no", status=0)
> to the end of the R script to ensure that the script exits with status
> code 0, but that did not change the error I got.
>
> So I am not sure how to solve this. The script works exactly as it's
> supposed to and creates the desired output, but tells me there is an
> error, and gives no way through the web interface to retrive the
> created output file.
>
> Also, I found out why two jobs were started each time I click
> "Execute". It's because I had two files in my <outputs> section:
>
>  <outputs>
>    <data format="pdf" name="out_file1" />
>    <data format="csv" name="out_file2" />
>  </outputs>
>
> Because my script generates two output files, a csv and a PDF. I took
> out the first <data> line above, and stopped passing the corresponding
> argument to my script, and the script no longer creates the PDF. Now
> the job only runs once each time I click "Execute". But I would like
> the script to once again produce both output files.
>
> So, perhaps it was doing the right thing all along...showing one
> dataset in the history panel for each output file produced.
>
> Looking through the galaxy distribution, I see at least one other tool
> that does the same thing. So, sorry for the noise on this.
>
> In any case, I still get the same error described above even when only
> one output file is produced.
>
> Thanks,
> Dan
>
>
>>
>>> I hope this get's you a little bit further.
>>
>>
>> Thanks much,
>> Dan
>>
>>
>>>
>>>
>>> Regards, Hans
>>>
>>>
>>>
>>>
>>>
>>> On 04/24/2012 11:56 PM, Dan Tenenbaum wrote:
>>>>
>>>> Apologies for originally posting this to galaxy-user; now I realize it
>>>> belongs here.
>>>>
>>>> Hello,
>>>>
>>>> I'm a galaxy newbie and running into several issues trying to adapt an
>>>> R script to be a galaxy tool.
>>>>
>>>> I'm looking at the XY plotting tool for guidance
>>>> (tools/plot/xy_plot.xml), but I decided not to embed my script in XML,
>>>> but instead have it in a separate script file, that way I can still
>>>> run it from the command line and make sure it works as I make
>>>> incremental changes. (So my script starts with args<-
>>>> commandArgs(TRUE)). Also, if it doesn't work, this suggests to me that
>>>> there is a problem with my galaxy configuration.
>>>>
>>>> First, I tried using the r_wrapper.sh script that comes with the XY
>>>> plotting tool,  but it threw away my arguments:
>>>>
>>>> An error occurred running this job: ARGUMENT
>>>> '/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_4.dat'
>>>> __ignored__
>>>>
>>>> ARGUMENT
>>>> '/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_3.dat'
>>>> __ignored__
>>>>
>>>> ARGUMENT 'Fly' __ignored__
>>>>
>>>> ARGUMENT 'Tagwise' __ignored__
>>>>
>>>> etc.
>>>>
>>>> So then I tried just switching to Rscript:
>>>>
>>>>   <command interpreter="bash">Rscript RNASeq.R $countsTsv $designTsv
>>>> "$organism" $dispersion $minimumCountsPerMillion
>>>> $minimumSamplesPerTranscript $out_file1 $out_file2</command>
>>>>
>>>> (My script produces as output a csv file and a pdf file. The final two
>>>> arguments I'm passing are the names of those files.)
>>>>
>>>> But then I get an error that Rscript can't be found.
>>>>
>>>> So I wrote a little wrapper script, Rscript_wrapper.sh:
>>>>
>>>> #!/bin/sh
>>>>
>>>> Rscript $*
>>>>
>>>> And called that:
>>>>   <command interpreter="bash">Rscript_wrapper.sh RNASeq.R $countsTsv
>>>> $designTsv "$organism" $dispersion $minimumCountsPerMillion
>>>> $minimumSamplesPerTranscript $out_file1 $out_file2</command>
>>>>
>>>> Then I got an error that RNASeq.R could not be found.
>>>>
>>>> So then I added the absolute path to my R script to the<command>  tag.
>>>> This seemed to work (that is, it got me further, to the next error),
>>>> but I'm not sure why I had to do this; in all the other tools I'm
>>>> looking at, the directory to the script to run does not have to be
>>>> specified; I assumed that the command would run in the appropriate
>>>> directory.
>>>>
>>>> So now I've specified the full path to my R script:
>>>>
>>>>   <command interpreter="bash">Rscript_wrapper.sh
>>>> /Users/dtenenba/dev/galaxy-dist/tools/bioc/RNASeq.R $countsTsv
>>>> $designTsv "$organism" $dispersion $minimumCountsPerMillion
>>>> $minimumSamplesPerTranscript $out_file1 $out_file2</command>
>>>>
>>>> And I get the following long error, which includes all of the output
>>>> of my R script:
>>>>
>>>> Traceback (most recent call last):
>>>>   File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/local.py",
>>>> line 133, in run_job
>>>>     job_wrapper.finish( stdout, stderr )
>>>>   File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/__init__.py",
>>>> line 725, in finish
>>>>     self.sa_session.flush()
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/scoping.py",
>>>> line 127, in do
>>>>     return getattr(self.registry(), name)(*args, **kwargs)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py",
>>>> line 1356, in flush
>>>>     self._flush(objects)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py",
>>>> line 1434, in _flush
>>>>     flush_context.execute()
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py",
>>>> line 261, in execute
>>>>     UOWExecutor().execute(self, tasks)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py",
>>>> line 753, in execute
>>>>     self.execute_save_steps(trans, task)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py",
>>>> line 768, in execute_save_steps
>>>>     self.save_objects(trans, task)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py",
>>>> line 759, in save_objects
>>>>     task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py",
>>>> line 1413, in _save_obj
>>>>     c = connection.execute(statement.values(value_params), params)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py",
>>>> line 824, in execute
>>>>     return Connection.executors[c](self, object, multiparams, params)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py",
>>>> line 874, in _execute_clauseelement
>>>>     return self.__execute_context(context)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py",
>>>> line 896, in __execute_context
>>>>     self._cursor_execute(context.cursor, context.statement,
>>>> context.parameters[0], context=context)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py",
>>>> line 950, in _cursor_execute
>>>>     self._handle_dbapi_exception(e, statement, parameters, cursor,
>>>> context)
>>>>   File
>>>> "/Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py",
>>>> line 931, in _handle_dbapi_exception
>>>>     raise exc.DBAPIError.instance(statement, parameters, e,
>>>> connection_invalidated=is_disconnect)
>>>> ProgrammingError: (ProgrammingError) You must not use 8-bit
>>>> bytestrings unless you use a text_factory that can interpret 8-bit
>>>> bytestrings (like text_factory = str). It is highly recommended that
>>>> you instead just switch your application to Unicode strings. u'UPDATE
>>>> job SET update_time=?, stdout=?, stderr=? WHERE job.id = ?'
>>>> ['2012-04-24 18:55:45.791417', '', 'BiocInstaller version 1.5.7,
>>>> ?biocLite for help\nWarning message:\nNAs introduced by coercion
>>>> \nLoading required package: methods\nLoading required package:
>>>> limma\nLoading required package: BiasedUrn\nLoading required package:
>>>> geneLenDataBase\nLoading required package: org.Dm.eg.db\nLoading
>>>> required package: AnnotationDbi\nLoading required package:
>>>> BiocGenerics\n\nAttaching package:
>>>> \xe2\x80\x98BiocGenerics\xe2\x80\x99\n\nThe following object(s) are
>>>> masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n\n    xtabs\n\nThe
>>>> following object(s) are masked from
>>>> \xe2\x80\x98package:base\xe2\x80\x99:\n\n    anyDuplicated, cbind,
>>>> colnames, duplicated, eval, Filter, Find,\n    get, intersect, lapply,
>>>> Map, mapply, mget, order, paste, pmax,\n    pmax.int, pmin, pmin.int,
>>>> Position, rbind, Reduce, rep.int,\n    rownames, sapply, setdiff,
>>>> table, tapply, union, unique\n\nLoading required package:
>>>> Biobase\nWelcome to Bioconductor\n\n    Vignettes contain introductory
>>>> material; view with\n    \'browseVignettes()\'. To cite Bioconductor,
>>>> see\n    \'citation("Biobase")\', and for packages
>>>> \'citation("pkgname")\'.\n\nLoading required package:
>>>> DBI\n\nCalculating library sizes from column totals.\nError in
>>>> matrix(u, nrow = nrows, byrow = TRUE) : \n  negative extents to
>>>> matrix\nCalls: plotMDS.DGEList ... equalizeLibSizes ->  splitIntoGroups
>>>> ->  lapply ->  FUN ->  matrix\nExecution halted\n', 15]
>>>>
>>>> Note that if I run my script from the command line:
>>>>
>>>> ./Rscript_wrapper.sh RNASeq.R
>>>> /Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_4.dat
>>>> /Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_3.dat Fly 1
>>>> 1 Tagwise MDSPlot.pdf outputs.csv
>>>>
>>>> It works fine and does not produce a warning about "NAs introduced by
>>>> coercion", nor does it fail with the "Error in matrix" above.
>>>>
>>>> So, can anyone tell me what is going wrong here? Why does R behave
>>>> differently in galaxy than it does on the command line? (I'm using the
>>>> same instance of R, same machine, for my galaxy and command-line
>>>> efforts). Is this 8-bit bytestring error a red herring? Can I filter
>>>> it so that galaxy is happy?
>>>>
>>>> Finally, one other curiosity. Every time I hit "Execute" in galaxy to
>>>> run my tool, it is run twice--two jobs are created (which each fail in
>>>> the same way). Why is this?
>>>>
>>>> My R script:
>>>> https://gist.github.com/2482783
>>>>
>>>> My XML file:
>>>> https://gist.github.com/2482792
>>>>
>>>> I can share more data (such as sample input files) if necessary.
>>>>
>>>> Thanks for your help.
>>>> Dan
>>>> ___________________________________________________________
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>>>>
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