Bioinformatics for Biologist: Installing NGS software

I remember I have difficulty install Velvet, the first Next Generation Sequencing software I use. As a biologist, I just don't understand how to install despite reading the manual many times. Once I did, NGS software installation becomes simple. Occasionally I run into problems. Maq and MapView are among the hardest softwares to install. Here, I'm gonna share how to install a NGS software.

Installation
The NGS softwares are compressed in a tar.gz file. Once downloaded, right click and select "Extract here". A folder with the same name will appear. It's your choice to install in which directory. Preferably in a hard disk (not Desktop or Documents) as the file generated will take a lot of space.

To install, ALWAYS read the manual or README.txt for instructions. Instructions differ for each software. Some softwares like Samtools are ready to run once unzipped. The two basic commands to install are:
> make
> make install

Here's an example, I just downloaded BWA 0.5.5 from http://sourceforge.net/projects/bio-bwa/files/. After unzipping it, I found no instruction to install. I thought it's ready to use. But command "./bwa" doesn't work. So I tried "make install" and "make". Only the latter works. During installation, there will be a long list in the Terminal to check if the required files/libraries/systems are present.

Once the installation completed, I type "./bwa". A help file with a list of options appeared. In bwa-0.5.5 folder, you will notice many files are added during installation. Mission accomplished.


Troubleshooting
When you fail to install it, the Terminal will show "ERROR" or "Stop". If you wanna know what went wrong, you need to check the lines that Terminal produces during Installation. Maybe you didn't install a library or some GNU environment required. Once missing components are identified, go to System > Administration > Synaptic package manager to install them. Try installation again.

Tutorial
Let's try installing maq-0.7.1. I have problem installing this version eventhough I was certain I have all the components installed. I even tried to install an older version 0.6.8 but it didn't work. Took me awhile to figure out what's missing.

For installation instruction, read http://maq.sourceforge.net/maq-man.shtml#install. To download, http://sourceforge.net/projects/maq/files/maq/

Why don't you try it on your own first. Just download the zip file, unpack it and simply type on Terminal:

./configure; make; make install

Alternatively, you can also type 3 separate commands:
>./configure
>make
>make install

If you manage to install it, congratulations! If you don't, welcome to the club!

OK. Let's cut the chase and tell you what I did to fix the problem. I realized a library known as "zlib1g-dev" is missing. After installing that library, I type:
>./configure
>make
>sudo make install
Then, type in administrator password and Wala!

Since I already install the library needed, I can't show you an example of failed installation. Oh this is the worst tutorial ever!