Installation section done.

doc/install.rst

@@ -5,15 +5,13 @@ System requirements
 -----------------------
 
 - Any Java-enabled platform (Windows, Linux, Mac OS X)
-- Java version 7 or higher (download from `Oracle web
-  site <http://www.oracle.com/technetwork/java/javase/downloads/index.html>`__)
+- Java version 7 or higher (download from `Oracle web site <http://www.oracle.com/technetwork/java/javase/downloads/index.html>`_)
 - 1--16 Gb RAM (depending on number of clones in the sample)
 
 Installation on Mac OS X / Linux
 ------------------------------------
 
-- Check that you have Java 1.7+ installed on your system by typing
-  ``java -version``. Here is the example output of this command:
+- Check that you have Java 1.7+ installed on your system by typing ``java -version``. Here is the example output of this command:
 
   .. code-block:: console
 
@@ -23,30 +21,32 @@ Installation on Mac OS X / Linux
     Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)
 
 - unzip the archive with MiXCR
-- add ``bin`` folder of MiXCR distribution to your ``PATH`` variable or
-  add symbolic link to ``mixcr`` script to the user folder with
-  executables (e.g. ``~/bin/`` in Ubuntu and many other popular linux
-  distributions)
+- add extracted folder of MiXCR distribution to your ``PATH`` variable or add symbolic link for ``mixcr`` script to your ``bin/`` folder (*e.g.* ``~/bin/`` in Ubuntu and many other popular linux distributions)
 
 Installation on Windows
 ---------------------------
 
-Currently there is no execution script or installer for Windows. Still
-MiXCR can easily be used by direct execution from the jar file.
+Currently there is no execution script or installer for Windows. Still MiXCR can easily be used by direct execution from the jar file.
 
--  check that you have Java 1.7+ installed on your system by typing
-   ``java -version``. Here is the example output of this command:
+- check that you have Java 1.7+ installed on your system by typing ``java -version``. Here is the example output of this command:
 
-``java version "1.7.0_65"    Java(TM) SE Runtime Environment (build 1.7.0_65-b17)    Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)``
+  .. code-block:: console
 
--  unzip the archive with MiXCR
--  use ``mixcr.jar`` from the ``jar`` folder in the following way:
+    > java -version
+    java version "1.7.0_65"
+    Java(TM) SE Runtime Environment (build 1.7.0_65-b17)
+    Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)
 
-``java -Xmx4g -Xms3g -jar path_to_mixcr\jar\mixcr.jar ...``
+- unzip the archive with MiXCR
+- use ``mixcr.jar`` from the archive in the following way:
+
+  .. code-block:: console
+    > java -Xmx4g -Xms3g -jar path_to_mixcr\jar\mixcr.jar ...
 
 For example:
 
-``java -Xmx4g -Xms3g -jar C:\path_to_mixcr\jar\mixcr.jar align input.fastq.gz output.vdjсa``
+  .. code-block:: console
+    > java -Xmx4g -Xms3g -jar C:\path_to_mixcr\jar\mixcr.jar align input.fastq.gz output.vdjсa
 
 To use mixcr from ``jar`` file one need to substitute ``mixcr`` command
 with ``java -Xmx4g -Xms3g -jar path_to_mixcr\jar\mixcr.jar`` in all