Hello everyone, I recently came across the MSGFgui packages for R (https://github.com/thomasp85/MSGFgui). I use command-line MS-GF+ regularly, but would like to utilize the visualization in the GUI. This is perhaps a long post, but please bear with me.
In R 3.2.3, I have installed MSGFplus and MSGFgui (and their dependencies) using biocLite.
I've loaded the program libraries using library(MSGFplus) followed by library(MSGFgui).
I can get the "web" interface to load in Google Chrome using MSGFgui().
However, when I actually attempt to run the GUI (i.e. load mzML and reference FASTA files, and hit "analyze"), it kicks the following error in my R console:
First time using MSGFplus: Downloading MS-GF+ code
trying URL 'http://proteomics.ucsd.edu/Software/MSGFPlus/MSGFPlus.20140630.zip'
Warning in download.file("http://proteomics.ucsd.edu/Software/MSGFPlus/MSGFPlus.20140630.zip", :
cannot open URL 'http://proteomics.ucsd.edu/Software/MSGFPlus/MSGFPlus.20140630.zip': HTTP status was '404 Not Found'
Warning: Unhandled error in observer: cannot open URL 'http://proteomics.ucsd.edu/Software/MSGFPlus/MSGFPlus.20140630.zip'
observe({
if (input$analysisButton == 0)
return(c())
if (input$analysisButton != analysisButtonCount) {
dataFiles <<- isolate({
datafileSelection()
})
currentPar <<- isolate({
par()
})
analysisButtonCount <<- input$analysisButton
currentAnalysis <<- runMSGF(currentPar, dataFiles[1],
async = TRUE)
progressBarData$max <<- length(dataFiles)
progressBarData$value <<- 1
session$sendCustomMessage(type = "progressBar", list(max = isolate({
progressBarData$max
}), value = isolate({
progressBarData$value
}) - 0.75, text = paste0("Analyzing ", basename(dataFiles[1])),
done = FALSE))
}
if (length(dataFiles)) {
if (finished(currentAnalysis)) {
session$sendCustomMessage(type = "progr [... truncated]
The output of sessionInfo() is:
R version 3.2.3 (2015-12-10) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.5 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] shiny_0.12.2 MSGFgui_1.4.0 xlsx_0.5.7 xlsxjars_0.6.1 rJava_0.9-7 [6] mzR_2.4.0 Rcpp_0.12.2 MSGFplus_1.4.0 BiocInstaller_1.20.1 loaded via a namespace (and not attached): [1] BiocGenerics_0.16.1 doParallel_1.0.10 xtable_1.8-0 R6_2.1.1 foreach_1.4.3 [6] plyr_1.8.3 tools_3.2.3 parallel_3.2.3 mzID_1.8.0 Biobase_2.30.0 [11] shinyFiles_0.6.0 htmltools_0.2.6 ProtGenerics_1.2.1 iterators_1.0.8 digest_0.6.8 [16] RJSONIO_1.3-0 codetools_0.2-14 mime_0.4 XML_3.98-1.3 jsonlite_0.9.19 [21] httpuv_1.3.3
It appears that MSGFgui is trying to get MSGFplus from a nonexistent source at UCSC. This seems odd, since I have installed MS-GF+ as a command-line program and (I think) as an R/bioconductor package. Is there a way to direct MSGFgui to the appropriate install location? I'd love to give this package a try for my research.
Thanks for your help!
It is not generally a good idea to install into a system.file location (I guess that's what is implied by the workaround?). It may not be writeable by non-administrative users.
I see your point, but I would argue (probably badly) that this type of package would always be user installed - i.e. located a place where the user has write access. I very much prefer to have all package related files in one place