Added some discussion of HPC specific issues to the teaching guide

_episodes/02-working-with-environments.md

@@ -21,7 +21,7 @@ objectives:
 keypoints:
 - "A Conda environment is a directory that contains a specific collection of Conda packages that you have installed."
 - "You create (remove) a new environment using the `conda create` (`conda remove`) commands."
-- "You activate (deactivate) an environment using the `conda activate` (`conda deactivate`) commands."
+- "You activate (deactivate) an environment using the `source activate` (`conda deactivate`) commands."
 - "You should install each environment as a sub-directory inside its corresponding project directory"
 - "Use the `conda env list` command to list existing environments and their respective locations."
 - "Use the `conda list` command to list all of the packages installed in an environment."
@@ -306,7 +306,7 @@ environments in your `~/miniconda3/env/` folder, you’ll have to give each of t
 > 
 > ~~~ 
 > $ cd my-project/
-> $ conda activate ./env
+> $ source activate ./env
 > ~~~
 > {: .language-bash}
 {: .callout}
@@ -374,7 +374,7 @@ you do not. Now your command prompt will display the active environment’s gene
  
 ~~~
 $ cd project-directory
-$ conda activate ./env
+$ source activate ./env
 (env) project-directory $
 ~~~
 {: .language-bash}
@@ -389,10 +389,10 @@ For more on modifying your `.condarc` file, see [the docs][conda-docs].
 > > ## Solution
 > > 
 > > You can activate an existing environment by providing the path the the environment directory 
-> > instead of the environment name when using the `conda activate` command as follows.
+> > instead of the environment name when using the `source activate` command as follows.
 > > 
 > > ~~~
-> > $ conda activate ./env
+> > $ source activate ./env
 > > ~~~
 > > {: .language-bash}
 > >

_episodes/03-sharing-environments.md

@@ -268,7 +268,7 @@ task.
 ~~~
 $ cd project-dir
 $ conda env create --prefix ./env --file environment.yml
-$ conda activate ./env
+$ source activate ./env
 ~~~
 {: .language-bash}
 

_extras/guide.md

@@ -1,6 +1,26 @@
 ---
 title: "Instructor Notes"
 ---
-FIXME
+
+## Conda on HPC systems
+
+Many HPC systems make either Miniconda or Anaconda (or both!) available to users via 
+[Environment Modules](http://modules.sourceforge.net/). In this case a user will need to load the 
+relevant module instead of installing Conda.
+
+~~~
+$ module load miniconda
+~~~
+{: .language-bash}
+
+> ## Avoid running the `conda init` command
+> 
+> Using the `conda init` command is not advisable on HPC systems that use Environment Modules 
+> to make Miniconda or Anaconda available to users.  The reason is that running the `conda init` 
+> command makes changes to a user's `~/.bashrc` file. If the user subsequently forgets to reverse 
+> these changes using `conda init --reverse`, then `conda` will still be available even after 
+> unloading or purging the `miniconda` module.  This opens the distinct possibility of a user 
+> accidently leaving his/her shell environment in an unexpected state.
+{: .callout}    
 
 {% include links.md %}