Impilo Central

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====== Installation of Mercator ======

===== Additional libraries =====

Some of Mercator's functions depend on some otehr applications **that are not present** in a basic Impilo install. \\Taken from the ''README'' file:
<code>
PREREQUISITES
-------------
In order to successfully compile the programs in this package, you
must have a couple of external packages installed.  These are:

- Optik: http://optik.sourceforge.net/
  - Only required if your version of python is < 2.3.
    This python library must be installed system-wide or in your
    personal python library directory (e.g. $HOME/lib/python).

- BLAT: http://www.cse.ucsc.edu/~kent/
  - Only required if you wish to generate input for the
    mercator program using the makeMercatorInput script.

- Genscan: http://genes.mit.edu/GENSCAN.html
  - Only required if you wish to run the makeMavidConstraints script
    for generating constraints for the MAVID multiple alignment
    program

- Polymake: http://www.math.tu-berlin.de/polymake/
  - Only required if you wish to build the parametricAlign program.
  - If installed, the environment variable POLYMAKE_PATH should be set
    to the directory in which you have installed the polymake package
    (using both the "make install" and "make install-devel" commands in
    the unpacked polymake directory)
</code>

If those functions are interesting for you, you will need to install them yourself in your local install or your virtual machine and rebuild Mercator from scratch. Sine a copy of this wiki is present on any Impilo install, don't forget to change this page too!!

===== Procédure =====

Here is the procedure to install Mercator from source code:

  * The source code archive has been downloaded from its web location, decompressed in ''/home/bioubuntu'' and moved into ''/opt/bio/sources/''.

  * The ''/opt/bio/sources/cndsrc-2009.11.17'' folder should belong to ''root'' and its permissions set to ''755''.

<code bash>
% sudo chown -R root:root /opt/bio/sources/cndsrc-2009.11.17
</code>

  * Once you are in ''/opt/bio/sources/cndsrc-2009.11.17'', compilation is easily done:

<code bash>
% sudo make
</code>

  * To make sure that anyone can use the application:

<code bash>
% sudo ln -s /opt/bio/sources/cndsrc-2009.11.17/apps/mercator /usr/local/bin/mercator
</code>