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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