Hi guys,
Following the instructions in the README.md file from the successful installation of the tool, I copied deseq.R to tool-data/
I've been trying to get the deseq_and_sam2counts tool on our local galaxy-dist here: http://toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts I note a prior message from Greg on certain <requirements> tags that should be added to get some things working in: http://dev.list.galaxyproject.org/environment-variables-and-paths-for-toolsh... It's probably not relevant to the error that I am getting at the moment since we've managed to install all those packages manually through R -
source("http://bioconductor.org/biocLite.R")
biocLite("DESeq") biocLite("aroma.light")
The following dataset was used:
dataset:
12345aba1345355777888aba24567888689
This is the error we get when running the tool. Note, it has executed the actual tool and made use of tool-data/deseq.R
29: Diagnostic Plots for DE Seq on data 27https://galaxy-qld-dev.genome.edu.au/history 0 bytes An error occurred running this job:*Error: Loading required package: Biobase Loading required package: BiocGenerics Loading required package: methods
Attaching package: ‘BiocGenerics’
The following object(s) are masked from ‘package:stats’:
xtabs
The following object(s) are* * * * *
Error: Loading required package: Biobase Loading required package: BiocGenerics Loading required package: methods Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: locfit locfit 1.5-8 2012-04-25 Loading required package: lattice Warning messages: 1: found methods to import for function ‘as.list’ but not the generic itself 2: found methods to import for function ‘eapply’ but not the generic itself Error in glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = c(0.1, : object 'fit' not found Calls: estimateDispersions ... parametricDispersionFit -> glm -> eval -> eval -> glm.fit In addition: Warning messages: 1: In is.na(rows) : is.na() applied to non-(list or vector) of type 'NULL' 2: In glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = c(0.1, : no observations informative at iteration 1
Any ideas?