[BioC] [devteam-bioc] Unable to

[Dan Tenenbaum]

On Tue, Feb 26, 2013 at 8:41 PM, Maintainer <maintainer at bioconductor.org> wrote:
>
> Hi there,
>
> I am new to Galaxy, and would like to create some tools that use some of my existing R scripts. I have played around with the example code, and have found this to be OK, however I am now having problems creating my own tools to use on Galaxy. My interest is in a user being able to upload a gene expression dataset, and then be able to carry out some functions using Galaxy for gene regulatory network inference and analysis.
>
> The first simple tool that I would like to create is a correlation matrix from a gene expression dataset that the user uploads to Galaxy. I have created the .Rd file, called corMat.Rd,which is as follows:
>
> \name{corMat}
> \alias{corMat}
> \title{a corMat function}
> \usage{
>   corMat(inputfile = GalaxyInputFile(),
>     outputfile = GalaxyOutput("mydata"," csv"))
> }
> \arguments{
>   \item{input}{An input dataset}
>
>   \item{output}{the output}
> }
> \description{
>   A correlation matrix function
> }
> \details{
>   nothing
> }
>
>
> I then defined the corMat function in R, which is as follows:
>
> corMat <- function (inputfile = GalaxyInputFile(),
> outputfile = GalaxyOutput("mydata", "csv"))
> {
>     data1 <- tryCatch({
>         as.matrix(read.delim(inputfile1, row.names = 1))
>     }, error = function(err) {
>         stop("failed to read first data file: ", conditionMessage(err))
>     })
>
>     data2 <- cor(data1)
>     write.csv(data2, file = outputfile)
> }
>
> To carry this out, I wish to use the cor function in the package WGCNA, so I then have put the following code into R:
>
> galaxy(
> corMat,
> manpage="/home/adminuser/galaxy-dist/tools/Network/corMat.Rd",
> package="WGCNA",
> is.exported="TRUE",
> version="0.1",
> name="Correlation Matrix",
> galaxyConfig=GalaxyConfig(
> galaxyHome=path.expand("~/galaxy-dist"),
> toolDir="tools/Network",
> sectionName="Network",
> sectionId="NetworkId")
> )
>
> However, this does not compile, and gives me the error message:
>
> Error in newXMLTextNode(title) :
>   CHAR() can only be applied to a 'CHARSXP', not a 'NULL'
>
> This error seems to occur when I change the name of the package from RGalaxy to anything else, however I need to change this to WGCNA to specify where to find the function cor that I use in the corMat function I have written for Galaxy. I am obviously making a mistake somewhere, however I cannot see where this error is.


The 'package' argument to galaxy() is asking you what package your
'Galaxy-enabled' function is in, in this case the function corMat(),
which you list above.
That function should have
library(WGCNA)
in its body.

>Would you be able to help me with this? I can see the power of having a web based user interface that can carry out powerful and intensive biomedical applications in an easy to use format, so am keen to get this to work.
>
>
> Kind regards,
>
> Alex
>
>  -- output of sessionInfo():
>
> R version 2.14.1 (2011-12-22)


RGalaxy should not be run in this version of R. It was part of the
Bioconductor 2.11 release, which means it should only be used with R
2.15 or higher.

Dan



> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
>  [1] parallel  splines   tools     stats     graphics  grDevices
>  [7] utils     datasets  methods   base
>
> other attached packages:
>  [1] WGCNA_1.25-2        doParallel_1.0.1    iterators_1.0.6
>  [4] foreach_1.4.0       MASS_7.3-16         reshape_0.8.4
>  [7] plyr_1.8            cluster_1.14.1      Hmisc_3.10-1
> [10] survival_2.36-10    flashClust_1.01-2   dynamicTreeCut_1.21
> [13] impute_1.28.0       RGalaxy_1.0.0       digest_0.6.3
> [16] optparse_1.0.1      XML_3.95-0.1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.14.0     BiocGenerics_0.4.0 brew_1.0-6
> [4] codetools_0.2-8    getopt_1.19.0      grid_2.14.1
> [7] lattice_0.20-0     roxygen2_2.2.2     stringr_0.6.2
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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