Unable to install SNPhylo in ubuntu

Question

[sukesh1411]

Hi

I am trying to generate phylogenetic tree for 40 genome rice varieties using SNPhylo program . I could not install SNPhylo program successfully in ubuntu. I could install all the dependent programs except R packages (gdsfmt, SNPRelate). When i try installing these packages manually the packages are saving in temp directory. During SNPhylo installation i need to mention the path where each software is installed. SNPhylo software could not detect the R package which is installed in temp directory. Is it possible for me to select the desired directory for installing the R packages. I tried several options, it might be simple mistake, please help me to install SNPhylo program

Answer 1

[leeandroid]

I don't know if I fully understand what you mean but I believe that the problem is the R installation. Can you run R? If so, when installing SNPhylo you just have to give the full path to the R binary file, usually at /bin directory.

Hope it helps.

[sukesh1411]

Thanks for your reply. I tried but it could not find necessary R packages when installing SNPhylo. Please check the error. ![[1]: https://imgur.com/a/6oCpO][1]

Answer 2

[leeandroid]

You should install them by opening R and paste (one at a time) the following:

install.packages("getopt", repos="http://cran.r-project.org")

install.packages("phangorn", repos="http://cran.r-project.org")

source("http://bioconductor.org/biocLite.R")

biocLite("gdsfmt")

biocLite("SNPRelate")