This page was last updated on Wednesday, 21-Dec-2016 14:04:16 CST

Installation notes for SNPhylo ver. 20160204

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Prerequisites

• Python
• MUSCLE
• dnaml, part of PHYLIP
• R
• R packages phangorn, gdsfmt, SNPRelate, and getopt
  
  1. $ sudo R
  2. > install.packages("getopt", repos="http://cran.r-project.org")
  3. > install.packages("phangorn", repos="http://cran.r-project.org")
  4. > source("http://bioconductor.org/biocLite.R")
  5. > biocLite("gdsfmt")
  6. > biocLite("SNPRelate")

Installation

1. $ ver="20160204"
2. $ cd /programinstallers/
3. $ wget -N http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz
4. Version not in file name, so rename it
   $ mv snphylo.tar.gz snphylo-$ver.tar.gz
5. $ cd /usr/local/bin
6. $ sudo tar -zxvf /programinstallers/snphylo-$ver.tar.gz
7. $ cd SNPhylo
8. $ sudo bash setup.sh
   Note the discrepancy in the version number below, it is hardcoded in the script and appears that it was not updated properly.
   Also, dnaml was in the PATH but for some reason was not detected

   Version: 20141127
   
   START TO SET UP FOR SNPHYLO!!!
   
   The detected path of R is /usr/bin/R. Is it correct? [Y/n] y
   
   The detected path of python is /usr/bin/python. Is it correct? [Y/n] y
   
   The detected path of muscle is /usr/local/bin/muscle. Is it correct? [Y/n] y
   
   dnaml is not found. Is the program already installed? [y/N] y
   Please enter the path of dnaml program (ex: /home/foo/bin/dnaml): /usr/local/bin/phylip/dnaml
   
   SNPHYLO is successfully installed!!!

9. Add to default PATH for all users
   $ sudo nano /etc/profile
   …
   PATH="$PATH:/usr/local/bin/SNPhylo"
   …