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4.8 years ago by
Guest User12k
Guest User12k 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. 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) 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.
ADD COMMENTlink modified 4.8 years ago by Dan Tenenbaum ♦♦ 8.2k • written 4.8 years ago by Guest User12k
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gravatar for Dan Tenenbaum
4.8 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
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. > > ____________________________________________________________________ ____ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave at lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc
ADD COMMENTlink written 4.8 years ago by Dan Tenenbaum ♦♦ 8.2k
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