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daafda5 Jan 3, 2013
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Installation

These instructions are for installing Evident natively. If you are looking for the fastest way to start using Evident check the virtual machine install instructions.

E-vident is written in Python, using QIIME as a base framework and the Apache HTTP Server. The following installation instructions assume all of these dependencies to be correctly installed.

Clone the E-vident repository from the GitHub repository site:

git clone git@github.com/qiime/evident.git ~/git_sw/evident

To access all the sample data contained in the repository, you will need to create a symbolic link from the repository you just downloaded to the root directory and name it /evident, for example:

sudo ln -s /Users/yoshiki/git_sw/evident/data /evident

The following steps will guide you through the installation and configuration of mod_python.

Modpython is an Apache module that embeds the Python interpreter within the server. To get the package you will need to download the most recent SVN version by running the following command:

svn co https://svn.apache.org/repos/asf/quetzalcoatl/mod_python/trunk modpython

The installation of mod_python varies depending on the OS version you are using.

Mac OS X 10.6.x Snow Leopard

Before proceeding, you will need to have the Apple Developer tools installed; these tools can be found in the installation CDs that ship with you computer. If you have Xcode installed in your computer it is very likely that you have the tools already.

cd modpython
./configure --with-apxs=/usr/sbin/apxs
make

make clean
make 
sudo make install

Mac OS X 10.7.x Lion and 10.8.x Mountain Lion

To proceed with this installation you will need to have installed Xcode (which you can download from the Mac App Store) after you have done this, the next step is to install the command line tools for OS X. Once this is done you can proceed to build the package.

cd modpython
./configure --with-apxs=/usr/sbin/apxs
make

Ubuntu

If you don't have Apache installed already proceed to install it and then install mod_python:

sudo apt-get install apache2
sudo apt-get install libapache2-mod-python libapache2-mod-python-doc

Configuration

The last few steps require you to modify your Apache configuration files located in:

  • Mac OS X /etc/apache2/httpd.conf
  • Ubuntu /etc/apache2/apache.conf

You will need to add all of the following lines:

LoadModule python_module libexec/apache2/mod_python.so
AddHandler mod_python .psp
PythonHandler mod_python.psp
PythonDebug On
PYTHONPATH "['/Users/yoshiki/Applications/sw/pynast','/Users/yoshiki/Applications/sw/qiime/','/Users/yoshiki/Applications/sw/pycogent/','/Users/yoshiki/Applications/sw/numpy/','/Users/yoshiki/Applications/sw/biom-format','/Users/yoshiki/Applications/sw/matplotlib/']+sys.path" 

Notice that on the last line each path corresponds to a python module that you should have installed in your computer, as an example here all our python modules are living under /Users/yoshiki/Applications/sw/ hence we have to add the location of each module.

It is possible however that if you have all this modules installed in the site-packages directory of your python installation folder, if this is the case you won't have individual folders per module and you will not need to add all these paths as python should automatically be able to see the information.

Now edit /private/etc/apache2/users/[username].conf to add the following lines:

<Directory "/Users/[username]/Sites/">
    Options Indexes MultiViews FollowSymLinks
    AllowOverride None
    Order allow,deny
    Allow from all
</Directory>

Restart Apache and now you should be all set.

Installation FAQs & Issues

Some of the known issues when building this package are:

llvm-gcc-4.2: error trying to exec '/Developer/usr/bin/../llvm-gcc-4.2/bin/powerpc-apple-darwin10-llvm-gcc-4.2': execvp: No such file or directory
lipo: can't figure out the architecture type of:

To overcome this issue you will need to install Xcode 3.2.1. Once this is installed, go to the mod-python directory and try to re-build the package:


error: command gcc-4.2 failed with exit status 1

Locate GCC by running which gcc from the terminal and create a symbolic link, for example:

$ which gcc
/usr/bin/gcc
$ sudo ln -s /usr/bin/gcc /usr/bin/gcc-4.2

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