Installation instructions for SAMtools 0.1.8

You need to install the following libraries:

• libncurses-dev

% sudo apt-get install -y libncurses-dev

To install SAMtools from source code, you need to follow this recipe:

• The archive with the source code was downloaded from the web site and decompressed in /home/bioubuntu:

% tar -jxvf samtools-0.1.8.tar.bz2

• Warning!! If you are compiling SAMtools on a 64-bit platform and you want to use it in building the Staden package, you will need to modify the Makefile file. You will need to edit the following line:

# Before
CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc

# After
CFLAGS=		-g -Wall -O2 -m64 -fPIC #-arch ppc

• The newly created folder is moved under /opt/bio/sources. We need to make sure that it belongs to root and its permissions are set to 755:

% sudo mv samtools-0.1.8 /opt/bio/sources
% sudo chown -R root:root /opt/bio/sources/samtools-0.1.8
% sudo chmod 755 /opt/bio/sources/samtools-0.1.8

• Once you are in the folder, compilation is easily performed:

% cd /opt/bio/sources/samtools-0.1.8
% sudo make

• To make samtools available to all, you have to do this:

% sudo ln -s /opt/bio/sources/samtools-0.1.8/samtools /usr/local/bin/samtools