install_motifmatchr.md

Installation of motifmatchr on Centos

Motifmatchr was used for benchmarking (it is not required for the use of SMEAGOL).

Below are listed the installation steps.

Centos packages

Install libraries that motifmatchr will assume are available on Centos:

sudo yum install libxml2-devel
sudo yum install libcurl-devel
sudo yum install openssl-devel
sudo yum install gsl-devel

R packages

Open R (we used ) and then follow the installation instructions below (after you have made sure that the above mentioned Centos libraries are installed).

> R.version
               _                           
platform       x86_64-redhat-linux-gnu     
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          6.0                         
year           2019                        
month          04                          
day            26                          
svn rev        76424                       
language       R                           
version.string R version 3.6.0 (2019-04-26)
nickname       Planting of a Tree          

The setting below will set repositories so that the "not available for R version" is largely not a problem anymore.

setRepositories(ind = c(1:6, 8))

To permanently change this, add a line like setRepositories(ind = c(1:6, 8)) to your Rprofile.site file. Source: https://stackoverflow.com/questions/25721884/how-should-i-deal-with-package-xxx-is-not-available-for-r-version-x-y-z-wa

Install R packages

install.packages("RCurl")
install.packages("CNEr")
BiocManager::install("motifmatchr")

To the request if any packages should be updated choose "all".

Load the R library

library(motifmatchr)