Let us run a few Linux commands to install a few software packages. Enter the following commands, and press y and enter when necessary. The instance that we have started is completely blank and does not contain any downloaded programs or software. We will need to build it up from scratch.
From yum (nmap): just to install a network tool
sudo yum install nmap
From source (seqtk):
sudo su -
yum install git
cd /usr/local/src
git clone https://github.com/lh3/seqtk.git
cd seqtk/
make
Whoops! That command failed. We’re still missing something. Now install gcc zlib-devel:
yum install gcc zlib-devel
make
Now the command should be recognized! There we go. Try seqtk again:
./seqtk
As you can see, the default “base” images are exactly that - clean initial installations of just the operating system. These are perfect for customizing so that you have exactly the software you might need - but some setup will be required. Another option is to use an AMI (Amazon Machine Image) that already has some software installed. We’ve made our lab’s AMI, which has quite a bit of genomics sofware pre-installed, available for all to use. We’ll do this in the next section.