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README.html
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<h1 id="fpocket-r">fpocket-R</h1>
<p>fpocket-R is a modified version of <a href="https://github.com/Discngine/fpocket">fpocket 4.0</a> and is optimized for finding, characterizing, and visulizing drug-like RNA-ligand binding pockets.</p>
<h2 id="installation-with-conda">Installation with Conda</h2>
<h3 id="windows-users">Windows Users:</h3>
<ol>
<li>
<p>fpocket-R requires a Unix/Linux to run properly, this mean that Windows users need to activate the Windows Subsystem for Linux (WSL).</p>
<ul>
<li>
<p>WSL is build-in to Windows 10 and 11 and allows users to easily run conda and fpocket-R using a Linux virtual machine.</p>
</li>
<li>
<p><a href="https://www.freecodecamp.org/news/how-to-install-wsl2-windows-subsystem-for-linux-2-on-windows-10/">Guide to installing WSL and Ubuntu</a></p>
</li>
<li>
<p>Once WSL is activated on your computer, use WSL/Ubuntu to install conda and fpocket-R using the installation instructions for Linux.</p>
</li>
</ul>
</li>
</ol>
<h3 id="linux-unix-macos-and-wsl-users">Linux, Unix, MacOS, and WSL users:</h3>
<ol start="2">
<li>
<p>Install conda on a Unix/Linux-based system</p>
<ul>
<li><a href="https://conda.io/projects/conda/en/latest/user-guide/install/index.html">Guide to install conda</a>
<ul>
<li>
<p><strong>macOS users:</strong> Regular installation > macOS</p>
</li>
<li>
<p><strong>Windows users:</strong> User WSL/Ubuntu to install conda: Regular installation > Linux</p>
</li>
<li>
<p><strong>Linux users:</strong> You can figure it out</p>
</li>
</ul>
</li>
</ul>
</li>
</ol>
<h3 id="linux-unix-macos-and-wsl-users-with-conda-installed">Linux, Unix, MacOS, and WSL users with conda installed:</h3>
<ol start="3">
<li>
<p>Open your terminal and navigate to the directory where you would like to install the fpocket-R and RNAvigate packages (optional).</p>
<ul>
<li>
<p><strong>Tip for new Windows (WSL) users:</strong> You can navigate to your Windows file system in the WSL command line by using the following command:</p>
<pre><code>cd /mnt/c/Users/<your-user-name>
</code></pre>
</li>
</ul>
</li>
<li>
<p>Clone the RNAvigate and fpocket-R GitHub repositories. (RNAvigate is a dependancy for fpocket-R)</p>
<pre><code> git clone https://github.com/Weeks-UNC/RNAvigate.git
git clone https://github.com/Weeks-UNC/fpocketR.git
</code></pre>
</li>
<li>
<p>Create fpocket-R conda eviroment and install fpocket-R and RNAvigate.</p>
<pre><code> cd fpocketR
conda env create -f env.yml
conda activate fpocketR
conda develop .
cd ../RNAvigate
conda develop .
</code></pre>
</li>
</ol>
<h2 id="demo">Demo</h2>
<p><a href="https://github.com/Weeks-UNC/fpocketR/blob/main/Demo/fpocketR_demo.md">Demonstration of fpocketR usage</a></p>
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