Instruction for Setup of OrthoMCL and its enviroment

# DISCLAIMER: 
Parts of the instruction are updated and revised copy from the original instruction from orthomcl.org and the 
repository of github user username juanu. Citations will be at the end of the file. 

## System requirement (cited from the orthomcl website):

(1) UNIX
  - The OrthoMCL Pairs program has only been tested on UNIX, specifically RedHat 5.8.  
  Other UNIX variants may work, but we can't support them.
  - The MCL program is UNIX compatible only

(2) BLAST
  - we recommend NCBI BLAST for two reasons
     a) theoretically: XXXXXXX
     b) practically: NCBI BLAST supports a tab delimited output which we provide parsers for.  See Step 7 below.
  - for large datasets (e.g. 1M proteins) all-v-all BLAST will likely require a compute cluster.
    Otherwise, it could run for weeks or months. 

(3) Relational Database 
  - The OrthoMCL Pairs program runs in a relational database.  Supported vendors are:
     - Oracle
     - MySql
  - If you don't already have one of these installed, install MySql, which can be done for free 
    and without significant systems administration support.  (Follow the instructions we provide below.)
    ** construction of a database will be introduced in the next section **
   We realize that it is a little inconvenient to require a relational database.  
   However, using a relational database as the core technology for orthomclPairs provides speed, 
   robustness and scalability that would have been very hard to acheive without it.
  - To Create a Database in Mysql(assume Mysql is licensed and installed on your lab computer):
    start Mysql: 
    ```
    mysql -u root -p
    ```
    then enter the password. 
    Once you got in. Do the following:
    ```sql
    CREATE DATABASE <database_name>
    ```
    Use the following to check if successfully created:
    ```sql
    SHOW DATABASES
    ```
    To fit in the context for a orthomcl software
    you need a database named 'orthomcl'
    !!!! exactly as it is!!! because the later schema and software will assume this database as the computation source!
    
(4) Hardware
  - the hardware requirements vary dramatically with the size of your dataset.
  - for the Benchmark Dataset, we recommend:
     - memory: at least 4G
     - disk: 100G free space.  
  - you can estimate your disk space needs more accurately when you have completed Step 8 below.
    You will need at least 5 times the size of the blast results file produced in that step.  
    90% of the disk space required is to hold that file, load it into the database and index it in the database.

(5) Perl
  - standard perl
  UNIX system has standard perl installed in the system, to check installation and version, use command line: 
  ```
  perl -v 
  ```
  - DBI libraries: the easier to install one is the one created by Tim Bunce and 
  could be found [here] (http://search.cpan.org/dist/DBI/lib/Bundle/DBI.pm).
  to install and auto-configure the dbi:
  ```
  perl -MCPAN -e 'install Bundle::DBI'
  ```
  Select sudo, unless you know how you want to customize it yourself. 
  
  
  

(6) MCL program
  - please see http://www.micans.org/mcl/sec_description1.html
  The installation steps are clear and correct as described on the webpage.

(7) Time
  - The Benchmark Dataset took:
    - 3 days to run all-v-all BLAST on a 500 cpu compute cluster.  
    - 16 hours for the orthmclPairs processing to find pairs
    - 2 hours for MCL to find the groups