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.cock@googlemail.com> wrote:

On Sun, Sep 29, 2013 at 8:47 PM, ruiwang.sz <ruiwang.sz@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