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<title>GLAM2 Installation</title>
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<h1>GLAM2 Installation</h1>
<h2>Requirements</h2>
<p>The only requirement is a C compiler. If you have some kind of Unix
or Linux system, you almost certainly have one already. If you have
Mac OS X, you may need to install a developer toolkit, which should
come for free with Mac OS X. If you have Windows, you can get a C
compiler from various places, such as <a
href="http://www.mingw.org/">MinGW</a> or <a
href="http://www.cygwin.com/">Cygwin</a>.</p>
<h2>Usual procedure</h2>
<p>This procedure should be suitable in most cases.</p>
<ol>
<li>You presumably obtained GLAM2 as a zipped package, called
something like glam2-9999.zip. The first step is to unzip it, creating
a new directory glam2-9999.</li>
<li>Using the command line, move into the src subdirectory and type
'make'. This should compile the glam2 programs.</li>
<li>To compile purge, move into the purge subdirectory and type
'make'.</li>
<li>After successful compilation, the programs are ready to use. Run
them just by typing their names (possibly with leading ./ depending on
the settings for your command line environment). If you like, you can
put the programs in standard 'bin' directories, or add their location
to your system's PATH.</li>
</ol>
<h2>Alternatives</h2>
<p>There is a <a href="http://packages.debian.org/glam2">Debian package</a>.</p>
<p>The Makefile in the src subdirectory holds the commands for
compiling the glam2 programs. (Likewise for the purge subdirectory.)
The commands are customized for the widely-used <a
href="http://gcc.gnu.org/">gcc</a> compiler. To use a different
compiler, you may have to modify the Makefile. The Makefile is very
simple and commented, so this should be doable even if you know
nothing about makefiles. However, you will obviously need to know what
commands are suitable for your compiler. Use compiler options that
make the resulting programs as fast as possible.</p>
<p>The programs can also be compiled directly, without 'make'. For
instance, to compile glam2mask, move into the src subdirectory and
type:</p>
<pre>
cc -Wall -O3 -o glam2mask glam2mask.c alignment.c fasta.c util.c -lm
</pre>
<p>Modify as appropriate for your compiler. Look in the Makefile for
commands to compile the other programs.</p>
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