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====== Installation instructions for SAMtools 0.1.8 ======

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

You need to install the following libraries:

  * ''libncurses-dev''

<code bash>
% sudo apt-get install -y libncurses-dev
</code>

===== Procedure =====

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'':

<code bash>
% tar -jxvf samtools-0.1.8.tar.bz2
</code>

  * **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:

<code bash>
# Before
CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
</code>

<code bash>
# After
CFLAGS=		-g -Wall -O2 -m64 -fPIC #-arch ppc
</code>

  * 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'':

<code bash>
% 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
</code>

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

<code bash>
% cd /opt/bio/sources/samtools-0.1.8
% sudo make
</code>

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

<code bash>
% sudo ln -s /opt/bio/sources/samtools-0.1.8/samtools /usr/local/bin/samtools
</code>