amending/adding installation instructions (fixes #141)

Author: cwehmeyer

Diff for: README.md

@@ -38,6 +38,8 @@ If you do not have conda, please follow the instructions here:
 
 https://conda.io/miniconda.html
 
+#### Installing the tutorials as a package
+
 After installing miniconda, you can install the tutorial either via
 
 ``` bash
@@ -56,6 +58,35 @@ If you intend to install with pip, for which can not give any support, you feel
 pip install git+https://github.com/markovmodel/pyemma_tutorials
 ```
 
+#### Manual installation
+
+If you wish to install the tutorial manually, you will need the following packages (including all their dependencies):
+
+- `pyemma`
+- `mdshare`
+- `nglview`
+- `nbexamples`
+- `jupyter_contrib_nbextensions`
+
+This can be done, for example, with conda:
+
+```bash
+conda install -c conda-forge pyemma mdshare nglview nbexamples jupyter_contrib_nbextensions
+```
+
+After installing `jupyter_contrib_nbextensions`, you need to activate the `toc2` and `exercise2` extensions:
+
+```bash
+jupyter nbextension enable toc2/main
+jupyter nbextension enable exercise2/main
+```
+
+Now all remains is to clone the repository to get the tutorial notebooks:
+
+```bash
+git clone https://github.com/markovmodel/pyemma_tutorials.git
+```
+
 ### Usage
 Now we have a fresh conda environment containing the notebooks and the software to run them. We can now just activate the environment and run the notebook server by invoking:
 
@@ -66,6 +97,18 @@ pyemma_tutorials
 
 The last command will start the notebook server and your browser should pop up pointing to a list of notebooks. You can choose either to preview or to create your own copy of the notebook. The latter will create a copy of the chosen notebook in your home directory, so your changes will not be lost after shutting down the notebook server.
 
+If you have a manual installation, move to the repository's notebook directory...
+
+```bash
+cd path_to_pyemma_tutorials/notebooks
+```
+
+... and start the notebook server there:
+
+```bash
+jupyter notebook
+```
+
 ### Deinstallation
 
 To uninstall you can remove the whole environment which will also uninstall the contained software again:
@@ -78,4 +121,3 @@ or if you have installed the package directly
 ``` bash
 conda remove pyemma_tutorials
 ```
-

Diff for: manuscript/manuscript.tex

@@ -102,8 +102,17 @@ \subsection{Software/system requirements}
 We utilize Jupyter~\cite{jupyter} notebooks to show code examples along with figures and interactive widgets to display molecules.
 The user can install all necessary packages in one step using the \texttt{conda} command provided by the Anaconda Python stack (\url{https://anaconda.com}).
 We recommend Anaconda because it resolves and installs dependencies as well as provides pre-compiled versions of common packages.
-
 The tutorial installation contains a launcher command to start the Jupyter notebook server as well as the notebook files.
+
+You can install the tutorial's dependencies in a new conda environment and start the notebook server via
+\begin{verbatim}
+conda create -n pyemma_tutorials
+conda activate pyemma_tutorials
+conda install -c conda-forge pyemma_tutorials
+pyemma_tutorials
+\end{verbatim}
+or refer to \githubrepository{} for more detailed installation and usage instructions.
+
 The data for the demonstrated test systems is downloaded upon the first use and is cached for future invocations of the tutorial.
 
 The underlying software stack for running the tutorial consists of: