diff --git a/docs/introduction/install/index.rst b/docs/introduction/install/index.rst
index 48adc5e97fb38ae2f5bfb87f0607cb4ecd6d289b..4917de4df661e118301d07f17cb084dff9c47edc 100644
--- a/docs/introduction/install/index.rst
+++ b/docs/introduction/install/index.rst
@@ -18,16 +18,19 @@ and follow instructions.
After adding the repositories to your package manager (read the instructed on the site)
You can install both `moose` and `moogli` using your package manager.
-On ``Debian/Ubuntu``::
+On ``Debian/Ubuntu``
+::
$ sudo apt-get install moose moogli
-On ``CentOS/RHEL/Fedora/Scientific Linux``::
+On ``CentOS/RHEL/Fedora/Scientific Linux``
+::
$ sudo yum install moose moogli
-On ``openSUSE``::
+On ``openSUSE``
+::
$ sudo zypper install moose moolgi
-.. todo:: gentoo, Arch Linux
+.. todo:: Packages for gentoo, Arch Linux
In case your distribution is not listed on `our repository page
<https://software.opensuse.org/download.html?project=home:moose&package=moose>`_
@@ -37,13 +40,15 @@ out the steps to build MOOSE from its source code.
Building MOOSE
--------------
-First, you need to get the source code. You can use ``git`` (to clone the whole
+First, you need to get the source code. You can use ``git`` (clone the
repository) or download snapshot of github repo by clicking on `this link
<https://github.com/BhallaLab/moose/archive/master.zip>`_.::
$ git clone https://github.com/BhallaLab/moose
-Or,::
+Or,
+::
$ wget https://github.com/BhallaLab/moose/archive/master.zip
+ $ unzip master.zip
If you don't want lasest snapshot of ``MOOSE``, you can download other released
versions from here `https://github.com/BhallaLab/moose/releases`.
@@ -53,44 +58,41 @@ Install dependencies
Next, you need to install required dependencies.
- cmake (version 2.8 or higher)
-- gsl-1.16 or higher `Source code <ftp://ftp.gnu.org/gnu/gsl/>`_.
+- gsl-1.16 or higher `download <ftp://ftp.gnu.org/gnu/gsl/>`_.
- libhdf5 development package.
-- libsbml (5.9.0, optional). You can download it from
- `here <https://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/>`_
+- libsbml (5.9.0, optional). `download <https://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/>`_
+- python development package
+- numpy
- Make sure that `libsml` is installed with `zlib` and `lxml` support.
- If you are using buildtools, then use the following to install libsbml::
+.. note::
+ `libsml` needs to be compiled with ``zlib`` and ``lxml`` support without
+ which, you might face link time errors. Following instructions are known to
+ work::
$ wget http://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/libSBML-5.9.0-core-src.tar.gz
$ tar -xzvf libSBML-5.9.0-core-src.tar.gz
$ cd libsbml-5.9.0
- $ ./configure --prefix=/usr --with-zlib --with-libxml
+ $ ./configure --with-zlib --with-libxml
$ make
$ sudo make install
-- python development package
-- numpy
+Most of the dependencies can be installed using package manager.
-On Ubuntu these can be installed by following command::
+On ``Debian/Ubuntu``
+::
$ sudo apt-get install libhdf5-dev cmake libgsl0-dev libpython-dev python-numpy
-On CentOS/Fedora/RHEL::
+.. note::
+ Ubuntu 12.04 does not have required version of ``gsl`` (required 1.16 or
+ higher, available 1.15). On Ubuntu 16.04, package name is ``libgsl-dev``.
+
+On ``CentOS/Fedora/RHEL/Scientific Linux``
+::
$ sudo yum install hdf5-devel cmake libgsl-dev python-devel python-numpy
-On OpenSUSE::
+On ``OpenSUSE``
+::
$ sudo zypper install hdf5-devel cmake libgsl-dev python-devel python-numpy
-For MOOSE Graphical User Interface (``moose-gui``), some additional dependencies
-are required
-
-- matplotlib
-- Python-qt4
-
-On Ubuntu/Debian, these can be installed with::
- $ sudo apt-get install python-matplotlib python-qt4
-
-On CentOS/Fedora/RHEL::
- $ sudo yum install python-matplotlib python-qt4
-
Now use `cmake` to build moose
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -105,50 +107,103 @@ Now use `cmake` to build moose
This will build pyMOOSE (MOOSE's python extention), `ctest` will run few tests to
check if build process was successful.
+.. note::
To install MOOSE into non-standard directory, pass additional argument
- `-DCMAKE_INSTALL_PREFIX=path/to/install/dir` to cmake e.g.
-
+ `-DCMAKE_INSTALL_PREFIX=path/to/install/dir` to cmake
+ ::
$ cmake -DCMAKE_INSTALL_PREFIC=$HOME/.local ..
- To use, different version of python,
-
+ To use different version of python
+ ::
$ cmake -DPYTHON_EXECUTABLE=/opt/python3/bin/python3 ..
-After that installation is pretty easy.
-
+After that installation is pretty easy
+::
$ sudo make install
If everything went fine, you should be able to import moose in python shell.
-.. codeblock:: python
- $ python
- >>> import moose
+.. code-block:: python
+ import moose
+
+
+Graphical User Interface (GUI)
+------------------------------
+
+You can get the source of ``moose-gui`` from `here
+<https://github.com/BhallaLab/moose-gui>`_. You can download it either by
+clicking on `this link <https://github.com/BhallaLab/moose-gui/archive/master.zip>`_
+or by using ``git`` ::
+ $ git clone https://github.com/BhallaLab/moose-gui
+
+To be able to launch ``moose-gui``, you need to install some more packages
+- matplotlib
+- python-qt4
+
+On ``Ubuntu/Debian``, these can be installed with
+::
+ $ sudo apt-get install python-matplotlib python-qt4
+
+On ``CentOS/Fedora/RHEL``
+::
+ $ sudo yum install python-matplotlib python-qt4
+
+Now you can fire up the GUI
+::
+ $ cd /to/moose-gui
+ $ python mgui.py
+
+.. note::
+ If you have installed ``moose`` using the package, then GUI is launched by
+ running following commnad::
+ $ moosegui
Building moogli
---------------
-Prefer the packages from the repository.
-
``moogli`` is subproject of ``MOOSE`` for visualizing models. More details can
-be found `here<http://moose.ncbs.res.in/moogli>`_.
+be found `here <http://moose.ncbs.res.in/moogli>`_.
+
+Prefer installing ``moogli`` packages from the repository as indicated on the
+top of this page. Link to ``moogli`` repository is given below
-Installing ``moogli`` could be tricky. It depends on ``OpenSceneGraph`` (version
-3.0.x) which not be easily available for your system. Depending on
-your distribution, you would need following packages to be installed.
+`https://software.opensuse.org/download.html?project=home%3Amoose&package=moogli`
-- Development package of libopenscenegraph
-- `libQGLViewer-2.3.15-py<https://gforge.inria.fr/frs/?group_id=773>`_. Install
-instructions `here<http://www.libqglviewer.com//installUnix.html#linux>`_.
+.. note::
+ If you have already added the repository, ``moogli`` is already available in
+ your package-manager.
-- `PyQGLViewer0.10<https://gforge.inria.fr/frs/?group_id=773>`_ (first install
-libQGLViewer-2.3.15-py) and untar contents::
- $ cd /path/to/PyQGLViewer0.10
- $ python setup.py build # to compile
- $ python setup.py install # to install on your system
- $ python setup.py bdist # to create a binary distribution
-On Ubuntu, following packages should suffice::
- $ sudo apt-get install python-qt4-dev python-qt4-gl libopenscenegraph-dev python-sip-dev
- libqt4-dev
+To get the latest source code of ``moogli``, click on `this link <https://github.com/BhallaLab/moogli/archive/master.zip>`_.
+
+Building ``moogli`` could be tricky. It depends on ``OpenSceneGraph`` (version
+3.2.0 or higher) which may not be easily available for your operating system.
+For this reason, we distribute required ``OpenSceneGraph`` with ``moogli``
+source code.
+
+Depending on distribution of your operating system, you would need following
+packages to be installed.
+
+On ``Ubuntu/Debian``
+::
+ $ sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev
+
+On ``Fedora/CentOS/RHEL``
+::
+ $ sudo yum install sip-devel PyQt4-devel qt4-devel libjpeg-devel PyQt4
+
+On ``openSUSE``
+::
+ $ sudo zypper install python-sip python-qt4-devel libqt4-devel python-qt4
+
+After this, building and installing ``moogli`` should be as simple as::
+ $ cd /path/to/moogli
+ $ mkdir _build
+ $ cd _build
+ $ cmake ..
+ $ make
+ $ sudo make install
+If you run into troubles, please report it on our `github repository
+<https://github.com/BhallaLab/moose/issues>`_.
diff --git a/docs/introduction/known_issues/index.rst b/docs/introduction/known_issues/index.rst
index 6d06e9b92977f18daccf1e3b7775afdbd1558bc4..73e6f3ef6e544b4f06b6df45423bdc4fc0302d5a 100644
--- a/docs/introduction/known_issues/index.rst
+++ b/docs/introduction/known_issues/index.rst
@@ -1,2 +1,9 @@
Known Issues and bugs
===================
+
+Full report can be found at following places
+
+- Related to build, packages and documentation `https://github.com/BhallaLab/moose/issues`
+- Related to python interface of MOOSE `https://github.com/BhallaLab/moose-core/issues`
+- Related to MOOSE GUI `https://github.com/BhallaLab/moose-gui/issues`
+- Related to ``moogli`` `https://github.com/BhallaLab/moogli/issues`