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
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to