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############
Installation
############
Before your start
=================
MHAP requires a recent version of the `JVM <http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html>`_ (1.8u6+). JDK 1.7 or earlier will not work. If you would like to build the code from source, you need to have the `JDK <http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html>`_ and the `Maven <https://maven.apache.org>`_ build system available.
Prerequisites
==============
* java (1.8u6+)
* maven (3.0+)
If you have not already installed the dependencies using maven, you will need an internet connection to do so during maven installation.
Here is a list of currently supported Operating Systems:
1. Mac OSX (10.7 or newer)
2. Linux 64-bit (tested on CentOS, Fedora, RedHat, OpenSUSE and Ubuntu)
3. Windows (XP or newer)
Installation
======================
Pre-compiled
-----------------
The pre-compiled version is recommended to users who want to run MHAP, without doing development. To download a pre-compiled tar run:
.. code-block:: bash
$ wget https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.jar.gz
And if ``wget`` not available, you can use ``curl`` instead:
.. code-block:: bash
$ curl -L https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.jar.gz
Then run
.. code-block:: bash
$ gunzip mhap-2.1.1.jar.gz
Now to run mhap
.. code-block:: bash
$ java -jar mhap-2.1.1.jar
Source
-----------------
To build the code from the release:
.. code-block:: bash
$ wget https://github.com/marbl/MHAP/archive/v2.1.1.zip
If you see a certificate not trusted error, you can add the following option to wget:
.. code-block:: bash
$ --no-check-certificate
And if ``wget`` not available, you can use ``curl`` instead:
.. code-block:: bash
$ curl -L https://github.com/marbl/MHAP/archive/v2.1.1.zip > v2.1.zip
You can also browse the https://github.com/marbl/MHAP/tree/v2.1.1
and click on Downloads.
Once downloaded, extract to unpack:
.. code-block:: bash
$ unzip v2.1.1.zip
Change to MASH directory:
.. code-block:: bash
$ cd MHAP-2.1.1
Once inside the directory, run:
.. code-block:: bash
$ maven install
This will compile the program and create a target/mhap-2.1.1.jar file which you can use to run MHAP. The quick-start instructions assume you are in the target directory when running the program. You can also use the target/mhap-2.1.1.jar file to copy MHAP to a different system or directory. If you would like to run the `validation utilties <utilities.html>`_ you must also download and build the `SSW Library <https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library>`_. Follow the instructions on the `utilities <utilities.html>`_ page.
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