Hi Peter,

Thanks! I got it working by putting a suppressMessages() around the
function call.

I might have some questions on how to generate output file names on the
fly...let me make some attempts
first. :-)

Best,
Rui


On Sun, Sep 29, 2013 at 10:54 PM, ruiwang.sz <ruiwang...@gmail.com> wrote:

> Hi Peter,
>
> Thanks for the reply.
>
> I checked the history view. I don't see anything when I clicked the "i"
> icon and click the stderr link. However, here is what I see if I click the
> little bug icon next to the "i":
>
>
> Tool execution generated the following error message:
>
> Loading required package: GenomicRanges
> Loading required package: methods
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>     clusterExport, clusterMap, parApply, parCapply, parLapply,
>     parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following object is masked from ‘package:stats’:
>
>     xtabs
>
> The following objects are masked from ‘package:base’:
>
>     anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval,
>     Filter, Find, get, intersect, lapply, Map, mapply, match, mget,
>     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
>     rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table,
>     tapply, union, unique, unlist
>
> Loading required package: IRanges
> 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: lattice
> Loading required package: Rcpp
> Loading required package: RcppArmadillo
> estimating size factors
> estimating dispersions
> gene-wise dispersion estimates
> mean-dispersion relationship
> final dispersion estimates
> fitting generalized linear model
>
> All these are the normal output message from loading the 'Deseq2' package
> in R, and run some functions. After I use
>
> suppressMessages(Library("DESeq2"))
>
> to suppress the library loading messages, now, the following lines appear
> if I click "i" and then click "stderr"
>
> estimating size factors
> estimating dispersions
> gene-wise dispersion estimates
> mean-dispersion relationship
> final dispersion estimates
> fitting generalized linear model
>
> I guess I need to suppress them as well -- but how come they are on stderr
> not stdout?
>
> Thanks,
> Rui
>
>
>
> On Sun, Sep 29, 2013 at 3:36 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:
>
>> On Sun, Sep 29, 2013 at 8:47 PM, ruiwang.sz <ruiwang...@gmail.com> wrote:
>> > Hi Guys,
>> >
>> > I'm doing a very simple test about deseq2...there is a weird situation
>> > always happening:
>> >
>> > It looks like the deseq2 tool executed just fine, without any error,
>> and the
>> > result files were created, but after the set_metadata, galaxy always
>> 'set
>> > dataset state to ERROR'.
>> >
>> > The xml file for this test is:
>> >
>> > <tool id="deseq2 test" name="DESeq2" version="2">
>> >   <description>Determines differentially expressed transcripts from read
>> > alignments</description>
>> >   <command>
>> >        t.sh $input1 $test $out $log
>> >     </command>
>> >   <inputs>
>> >     <param format="txt" name="input1" type="data" label="Quant"/>
>> >     <param format="txt" name="input2" type="data" label="Conditions"/>
>> >     <param name="test" type="select" label="please choose control
>> > condition">
>> >             <options from_dataset="input2">
>> >               <column name="value" index="0"/>
>> >             </options>
>> >    </param>
>> >   </inputs>
>> >
>> >   <outputs>
>> >     <data format="txt" name="out" label="DESeq result"/>
>> >     <data format="txt" name="log" label="DESeq log file"/>
>> >   </outputs>
>> > </tool>
>> >
>> > Basically, we have an input file from Partek flow(input1), input2 is one
>> > column
>> > from input1, which has all the conditions, in our test, it has 3
>> conditions,
>> > CTC, LM, PT.
>> >
>> > input name "test" is the dropdown list that contain all 3 conditions,
>> and we
>> > choose
>> > one as control condition, in our case it is CTC.
>> >
>> > t.sh is very simple, it basically calls R script:
>> >
>> > Rscript /home/bioinfo/app/galaxy-dist/tools/Deseq/workflow.R $1 $2 $3 $4
>> >
>> > now, in the workflow.R, the related output part is:
>> >
>> > for (i in 2:3) {
>> >   res <- results(dds, contrasts[i])
>> >
>> >   ## sort the result table by FDR
>> >   res <- res[order(res$padj),]
>> >
>> >   ## Output the results
>> >  write.table(as.data.frame(res), file=paste0(args[i+1]), sep = "\t")
>> > }
>> >
>> > So, it looks like the result files were generated as expected, with the
>> > correct information.
>> > However, it always was set to state ERROR. Am I missing something? Or
>> did
>> > anyone see this before?
>> >
>> > Any inputs will be greatly appreciated!
>> >
>> > Thanks,
>> > Rui
>>
>> Hi Rui,
>>
>> Was anything written to stderr, like a warning from R itself?
>> You should be able to check via the "i" icon of the dataset
>> in the history view.
>>
>> By default, Galaxy treats any output on stderr as an error,
>> see the <stdio> tag information here:
>> http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
>>
>> Peter
>>
>
>
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