docs: SCHWED-3097 More documentation

singularity/README.rst

 OST Singularity
 ===============
 
-Build Singularity image
------------------------
+Building Singularity image
+--------------------------
 
 In order to build OST Singularity image:
 
@@ -21,77 +21,42 @@ that the image name is `ost.img`.
 Available apps
 --------------
 
-OST
-===
+This container includes the following apps:
+ * **OST** - OpenStructure binary
+ * **IPython** - OST-powered iPython shell
+ * **Notebook** - A Jupyter notebook palyground with OST and nglview
+ * **lDDT** - The Local Distance Difference Test
+ * **Molck** - Molecular checker
+ * **ChemdictTool** - Creating or update a compound library
 
-The OST app exposes OpenStructure binary and can be used to run interactive shell
-and scripts.
-
-To invoke OST shell run:
+To see the help for each individual app run:
 
 .. code-block:: bash
-  singularity run --app OST ost.img
-
-In order to run OST script do:
-
-.. code-block:: bash
-  singularity run --app OST ost.img <SCRIPT NAME> [SCRIPT OPTIONS]
-
-.. warning::
 
-  If script requires some external files eg. PDBs, they have to be located in the
-  path accessible via mounted volumes. By default Singularity mounts $HOME and
-  goes to CWD. Thus this sould work as expected out of the box.
-
-One can find a exemplary script (`test_docker.py`) in the <OST ROOT>/docker
-directory. To run it do:
-
-.. code-block::
-
-  cd <OST ROOT>/singularity
-  singularity run --app OST ost.img ../docker/test_docker.py
+    singularity help --app <APP NAME> <PATH TO OST IMAGE>
 
-lDDT
-====
+Eg.:
 
-This app runs the Local Distance Test. To see more details run:
+.. code-block:: bash
 
-.. code-block::
+    singularity help --app OST ost.img
 
-  cd <OST ROOT>/singularity
-  singularity run --app lDDT ost.img
 
-Molck
-====
+Facilitating the usage
+----------------------
 
-This app runs the Local Distance Test. To see more details run:
+For each of these apps it is useful to create an alias if they will be
+frequently used. Eg. to create an alias for IPython app one can run:
 
 .. code-block::
 
-  cd <OST ROOT>/singularity
-  singularity run --app Molck ost.img
-
-Notebook
-========
+  alias ost_ipython="singularity run --app IPython <PATH TO OST IMAGE>"
 
-Probably the best way to play with OpenStructure is to run it wihtin the Jupyter
-notebook. In order to so run:
+Then (in the same terminal window) to invoke IPython app one can just type:
 
 .. code-block::
 
-  cd <OST ROOT>/singularity
-  singularity run --app Notebook ost.img
-
-Copy the URL to the browser and launch the notebook with OST kernel. This will
-load all necessary OST components just like in the OST shell. We also enabled
-the nglview widget to interactively view molecular structures and trajectories.
-For more details on how to use nglview see `the documentation 
-<http://nglviewer.org/nglview/latest/>`_.
-
-
-.. warning::
+  ost_ipython
 
-  As the Singularity mounts $HOME by default Jupyter and Ipython config files
-  are moved to separate directories. Proper environmental variables are also set.
-  In addition, Jupyter is run in a separate virtualenv to not interact with possibly
+To make the alias permanent put it into your `.bashrc` file or whatever file you
+use to store the aliases.
\ No newline at end of file
-  installed host version.

singularity/Singularity.1.7.1

@@ -378,6 +378,16 @@ Useful options when running on remote server:
         Default: 8888
         The port the notebook server will listen on.
 
+Copy the URL to the browser and launch the notebook with OST kernel. This will
+load all necessary OST components just like in the OST shell. We also enabled
+the nglview widget to interactively view molecular structures and trajectories.
+For more details on how to use nglview see http://nglviewer.org/nglview/latest/.
+
+As the Singularity mounts $HOME by default Jupyter and Ipython config files
+are moved to separate directories. Proper environmental variables are also set.
+In addition, Jupyter is run in a separate virtualenv to not interact with possibly
+installed host version.
+
 To list of all available options:
 
     singularity run --app Notebook <IMAGE> --help