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.sz@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.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