Please find the instructions for both exercises in a single PDF file, provided here.
We recommend to run both exercises through the Terminal (on Mac/Linux) of your own machine, connecting to the AMI with ssh. If you’re on Windows, please use PuTTY to do the same. You will find the files needed for the BayeScan exercise in ~/wpsg_2016/activities/bayescan, and those needed for the BayeScEnv exercise in ~/wpsg_2016/activities/bayescenv/. Please note that the input file for BayeScan HsIMM-Us100-2.txt somewhat accidentally ended up in the directory ~/wpsg_2016/activities/bayescenv/inputData/ rather than in the BayeScan directory. However, you will only need this input file if you’d actually like to run BayeScan to see the progress of the analysis. As the analysis will take much longer than we have time available though, this step is optional, and we have provided run results in each of the program directories.
Also, note that once you’re logged in to the AMI via ssh/PuTTY, you can execute the two programs simply by typing bayescan or bayescenv (using BayeScan2.1_macos64bits or BayeScan2.1_linux64bits instead of bayescan, as described in the instructions, will also work, but is not needed).
In order to run the R commands included in the exercise, we recommend the use of RStudio through your a browser on your own machine. To do so, please open either Firefox or Chrome and type http://THE_PUBLIC_DNS_OF_YOUR_AMI_INSTANCE:8787 (obviously, you’ll have to replace “THE_PUBLIC_DNS_OF_YOUR_AMI_INSTANCE” with the actual public DNS of your instance).