Installation¶

Prerequisites¶

Moa is developed and tested on Ubuntu and RHEL and is expected to operate without much problems on all modern Linux distributions. Moa has the following prerequisites (and a large number more for all templates). Version numbers are an indication, not strict prerequisites. Other, even older, versions might work.

Python (2.6 or 2.7). Moa will not work with versions earlier, or with 3.0 and up
Git (1.6). Necessary either to download the Moa software from github, or, to make use of the integrated version control.
A number of support scripts & templates depend on Biopython. Consider installing it before starting to use Moa.
Python-dev: the Python development package. A few prerequisites installed by easy_install try to compile C libraries, and need this. Although all of them have backup, python only, alteratives; from a performace perspective it is probably smart to have this installed:
```
sudo apt-get install python-dev
```
python-yaml:On ubuntu, this installs a fast YAML parser - using easy_install or pip might install a slower, python only, version:
```
sudo apt-get install python-yaml
```

Python prerequisites¶

These prereqs can be installed manually or with easy_install or pip:

pyyaml (unless already installed)
Jinja2
Ruffus
gitpython
`unittest2 http://pypi.python.org/pypi/unittest2`_
`lockfile http://pypi.python.org/pypi/lockfile`_

Not part of the list of prerequisites are the following libraries, which you’ll only need if you are planning to run the web interface:

Bioinformatics tools¶

Each of the wrapped tools requires the tools to be present. Usually, Moa expects all tools to be present & executable on the system PATH. The standard Moa distribution comes with wrappers for:

Blast
BWA
Bowtie
Soap

and many more

Installing git (from github)¶

Moa is hosted on, and can be installed from, github:

cd ~
git clone git://github.com/mfiers/Moa.git moa

Note - their is also a copy of moa in the python package index - this one is almost certainly outdated, and is currently not supported.

Configuration¶

Configuration of Moa is simple, and can be done by sourcing the moainit script:

. ~/moa/bin/moainit

(Note the dot!, alternatively use: source ~/moa/bin/moainit)

It is probably a good idea to add this line to your ~/.bashrc for future sessions.

Moa should now work, try moa –help.

If your default python version is NOT python2.6 or python2.7 there are a few options that you can pursue:

change the hashbang of the moa script
define an alias in your ~/.bashrc: alias moa=’python2.6 moa’
create a symlink to python2.6 in your ~/bin directory and make sure that that is first in your path.

Installing the web interface¶

Note - this is highly experimental - you will probably need to fiddle with the configuration files to get it working. Start with installing apache2.

Then - assuming that: * Your Moa work directory is under /home/moa/work * Your Moa is installed in /opt/moa Create a file in /etc/apache2/conf.d/moa.conf with the following approximate contents:

Alias /moa/data /home/moa/work
<Directory /home/moa/work>
   Options +Indexes +FollowSymLinks
   Order allow,deny
   Allow from all

   SetEnv MOADATAROOT /home/moa/work
   SetEnv MOAWEBROOT /moa/data

   IndexOptions FoldersFirst SuppressRules HTMLTable IconHeight=24 SuppressHTMLPreamble SuppressColumnSorting SuppressDescription

   HeaderName /moa/cgi/indexHeader.cgi
   ReadmeName /moa/html/indexFooter.html
</Directory>

ScriptAlias /moa/cgi/ /opt/moa/www/cgi/
<Directory /opt/moa/www/cgi/>
    AddType text/html .cgi
    Order allow,deny
    Allow from all
    SetEnv MOABASE /opt/moa
</Directory>

Alias /moa/html/ /opt/moa/www/html/
<Directory /opt/moa/www/html>
    Order allow,deny
    Allow from all
    Options +Indexes
</Directory>

You might want to check the #! of /opt/moa/www/cgi/indexHeader.cgi depending on your system configuration. Restart apache and it should work

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