To recreate the anlaysis used in the Anderson et al. manuscript, "Adaptation of the rumen microbiota during a finishing study", there are two steps (follow the guidelines below). All of the commands to generate the manuscript outputs have been ran on Mac OS X 10.9 (others systems should work fine) with 8 GB RAM. No root access is needed. This should all work in a linux enviornmnet as well if you use a linux version of USEARCH and the anaconda package manager download page. The only two dependencies I believe are X11 (remember if logging onto a server) and perl (version shouldnt matter).

1. Run the bash script to create a virtual enironment and download/install programs LOCALLY with the anaconda package manager. This will recreate the same enivronment I used.

2. Render the R Markdown file with knitR to recreate the workflow and outputs.

Due to licensing issues, USEARCH can not be included in the setup. To obtain a download link, go to the USEARCH download page and select version USEARCH v7.0.1090 for linux. A link (expires after 30 days) will be sent to the provided email. Use the link as an argument for shell script below.

Simply download the bash script from the github repository and run it (provide the link to download your licensed USEARCH version as an argument for setup.sh):

1. wget https://raw.githubusercontent.com/chrisLanderson/rumen_adaptation/master/setup.sh
2. chmod 775 setup.sh
3. ./setup.sh usearch_link

Anaconda is downloaded and prompts you during installataion of the packages above. The prompts are as follows:

1. Press enter to view the license agreement
2. Press enter to read the license and q to exit
3. Accept the terms
4. Prompts you where to install anaconda. Simply type anaconda to create a directory within the current directory. Should be: [/Users/user/anaconda] >>> anaconda
5. No to prepend anaconda to your path. Choosing yes should not impact the installation though.
6. Will be asked a few times if you wish to proceed with installing the packages...agree to it.
7. After installation, enter 'source anaconda/bin/activate rumenEnv' on the command line to activate the virtual enviornment with all dependencies.

To convert the R markdown to html use the command: render("rumen_adaptation.Rmd"). To start a R session and run the workflow, use these commands from within the direcotry you initiated installation:

1. source anaconda/bin/activate rumenEnv
2. R
3. install.packages("rmarkdown", repos='http://cran.us.r-project.org')
4. install.packages("knitr", repos='http://cran.us.r-project.org')
5. library(rmarkdown)
6. library(knitr)
7. render("rumen_adaptation.Rmd")

The rendered html version can be found here