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building_luciphor.html
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<html>
<head>
<title>Compiling Luciphor</title>
<style>
li {
margin: 20px;
line-height:25px;
}
p {
line-height:25px;
}
#warning {
color:red;
}
#code2 {
font-family:Monospace;
font-weight:bold;
font-size:120%;
}
#code {
margin: 20px, 20px;
padding: 2px 10px;
font-family:Monospace;
background-color:#F8F8F8;
}
#main {
margin: 40px, auto;
padding: 40px;
width: 940px;
}
</style>
</head>
<body>
<div id="main">
<h1>Compiling Luciphor with Proteowizard</h1>
<p>This tutorial covers how to compile Luciphor on Linux.
The instructions are written assuming you are using RHEL/CENTOS 6.3 or Fedora 17.
I don't use Ubuntu or any of the other flavors of Linux but I imagine these steps
are generally applicable to those distributions.
</p>
<ol>
<li>
Download the Luciphor source code from this site:
<a href="http://dfermin.github.com/luciphor">http://dfermin.github.com/luciphor</a><br/>
For this tutorial we'll assume you downloaded the tar.gz file.
</li>
<li>
Unpack the tarball. This should produce a folder named something like
<span id="code2">dfermin-luciphor-<d0f3388></span><br/>
The part that reads something like <i>d0f3388</i> changes with any updates to github so this
part can be different in your download.
</li>
<li>
Unpack and prep the Proteowizard library for compilation. The following commands should be
executed in order from <i>within</i> the dfermin-luciphor-<d0f3388><br/>
<div id="code">
mkdir pwiz_root<br/>
mv pwiz-src-without*.bz2 pwiz_root/<br/>
mv boost_1_43_0.tar.bz2 pwiz_root/<br/>
cd pwiz_root<br/>
tar xjf pwiz_src_without*.bz2<br/>
tar xjf boost_1_43_0.tar.bz2<br/>
</div>
</li>
<li>
Now we will compile Proteowizard.
<span id="warning"><i>WARNING: This will take a long time so be patient!</i></span><br/>
Within the pwiz_root folder, type:<br/>
<div id="code">
bash quickbuild.sh pwiz/data/msdata
</div><br/>
If you have a computer with multiple processors you can speed up the process by typing:<br/>
<div id="code">
bash quickbuild.sh pwiz/data/msdata -j<THREADS>
</div>
Where <span id="code2"><THREADS></span> is the number of processors
you want to use for building Proteowizard.<br/>
<br/>
Now back out of the <span id="code2">pwiz_root</span> folder.
You're done with the hardest part of this ordeal.
<div id="code">cd ..</div>
</li>
<li>
Assuming you compiled Proteowizard as described above. You should be able to generate
the luciphor executable by running:
<div id="code">
bash compile.sh
</div>
<br/>
Like Proteowizard you can specify the number of threads to use for compilation:
<div id="code">
bash compile.sh -j<THREADS>
</div>
<br/>Compilation will take some time so <span id="warning">be patient!</span><br/>
If all went well, you should find an executable program called <span id="code2">luciphor</span>
in the current directory.<br/>
For general usage instructions, execute luciphor and it will print out some (hopefully) useful information.
</li>
</ol>
<br/>
If you have questions or problems please post to our discussion forum at:<br/>
<span id="code2">[email protected]</span>
<br/>
</div>
</body>
</html>