1

doc/index.rst

@@ -6,4 +6,5 @@ MIXCR User Guide
 .. toctree::
    :maxdepth: 2
 
+   install
    manual

doc/install.rst

@@ -0,0 +1,53 @@
+Installation
+===============
+
+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>`__)
+- 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:
+
+  .. code-block:: console
+
+    > 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)
+
+- 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)
+
+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.
+
+-  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)``
+
+-  unzip the archive with MiXCR
+-  use ``mixcr.jar`` from the ``jar`` folder in the following way:
+
+``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``
+
+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
+examples from this manual.