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Update installation.rst
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konstantinberlin authored Oct 4, 2016
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18 changes: 9 additions & 9 deletions docs/source/installation.rst
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Expand Up @@ -28,19 +28,19 @@ The pre-compiled version is recommended to users who want to run MHAP, without d

.. code-block:: bash
$ wget https://github.com/marbl/MHAP/releases/download/v2.1/mhap-2.1.tar.gz
$ wget https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.tar.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/mhap-2.1.tar.gz > mhap-2.1.tar.gz
$ curl -L https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.tar.gz > mhap-2.1.1.tar.gz
Then run

.. code-block:: bash
$ tar xvzf mhap-2.1.tar.gz
$ tar xvzf mhap-2.1.1.tar.gz
Source
-----------------
Expand All @@ -49,7 +49,7 @@ To build the code from the release:

.. code-block:: bash
$ wget https://github.com/marbl/MHAP/archive/v2.1.zip
$ 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:

Expand All @@ -61,27 +61,27 @@ And if ``wget`` not available, you can use ``curl`` instead:

.. code-block:: bash
$ curl -L https://github.com/marbl/MHAP/archive/v2.1.zip > v2.1.zip
$ 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
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.zip
$ unzip v2.1.1.zip
Change to MASH directory:

.. code-block:: bash
$ cd MHAP-2.1
$ 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.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.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.
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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