Installing macqiime and R packages

Finally took the leap and did  “native” install of macqiime on my MacAir and iMac (fed up with using VirtualBox…).

Followed all the install instructions for Macqiime 1.7.0, available here. Some notes on the install

  • Downloaded the full suite of Greengenes files (gg_12_10) and moved into the /macqiime/greengenes/ root folder
  • Installed legacy BLAST 2.2.22 using the instructions here
  • Downloaded the 32-bit versions of usearch 5.2.236  (renamed “usearch”) and the usearch 6.1 executable (renamed “usearch61”); both of these I put in the /macqiime/bin/ root folder since that directory is already in my path.
  • Installed a whole bunch of R packages (after installing R from one of the links on this page: http://cran.r-project.org/mirrors.html and then installing RStudio from http://www.rstudio.com/ide/download/):
    • install.packages(“ggplot2”)
    • install.packages(“XML”)
    • install.packages(“tm”)
    • install.packages(“RCurl”)
    • install.packages(“plyr”)
    • install.packages(‘randomForest’)
    • install.packages(‘ape’)
    • install.packages(‘vegan’)
    • install.packages(‘optparse’)
    • install.packages(‘gtools’)
    • install.packages(‘klaR’)
    • install.packages(‘RColorBrewer’)
    • install.packages(“labdsv”)
  • Didn’t install AmpliconNoise – no more 454 data!!
  • Installed TopiaryExplorer (needed to install Java runtime environment on my MacAir)
  • Installed Cytoscape 3.01
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