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installing_RSAT_procedure.html
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<h1 class="title toc-ignore">Installing RSAT on a Unix operating system</h1>
<h4 class="author">Jacques van Helden</h4>
<h4 class="date">2020-01-04</h4>
</div>
<hr />
<div id="introduction" class="section level1">
<h1><span class="header-section-number">1</span> Introduction</h1>
<hr />
</div>
<div id="overview-of-the-installation-steps" class="section level1">
<h1><span class="header-section-number">2</span> Overview of the installation steps</h1>
<ol style="list-style-type: decimal">
<li>Download a tarball archive with RSAT code.</li>
<li>Configure your local installation.</li>
<li>If your OS is Ubuntu, run the installation bash scripts. If not some adaptation of these scripts will be necessary (e.g. system libraries).</li>
<li>Test the command lines</li>
<li>Test the Web server</li>
<li>Test the Web services (SOAP/WSDL and REST)</li>
</ol>
<hr />
</div>
<div id="downloading-rsat" class="section level1">
<h1><span class="header-section-number">3</span> Downloading RSAT</h1>
<ol style="list-style-type: decimal">
<li>Go to the RSAT portal (<strong><a href="http://rsat.eu/" class="uri">http://rsat.eu/</a></strong>)</li>
<li>Select any server.</li>
<li>In the left-sided menu, click on the <strong>Download</strong> link.</li>
<li>Fill in your name and coordinates and access to the download site.</li>
</ol>
<p>You now have access to the download page containing the links to</p>
<ul>
<li><p>the latest stable release named <code>rsat_20XX-XX-XX.tar.gz</code> (XX-XX-XX must be replaced by the release date).</p></li>
<li><p>the previous release archives available in the folder <code>previous_versions</code>.</p></li>
</ul>
<div id="downloading-the-latest-rsat-release-via-the-web-installer" class="section level2">
<h2><span class="header-section-number">3.1</span> Downloading the latest RSAT release via the Web installer</h2>
<ol start="5" style="list-style-type: decimal">
<li>Download the tar archive named</li>
</ol>
<p><code>rsat_20XX-XX-XX.tar.gz</code></p>
<p>where <code>XX-XX-XX</code> is the latest release date and put it in your chosen directory.</p>
<ol start="6" style="list-style-type: decimal">
<li>Uncompress the archive. This will create a directory named <code>rsat</code> where we will continue the install procedure.</li>
</ol>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="bu">export</span> <span class="va">RELEASE=</span>20XX.XX.XX</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co">## e.g. export RELEASE=2020.01.04</span></a>
<a class="sourceLine" id="cb1-3" data-line-number="3"></a>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co">## By default we install the package a folder named packages. </span></a>
<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="co">## This should be adapted according to your local setup. </span></a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="bu">export</span> <span class="va">INSTALL_ROOT=</span>~/packages</a>
<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="fu">mkdir</span> -p <span class="va">${INSTALL_ROOT}</span></a>
<a class="sourceLine" id="cb1-8" data-line-number="8"></a>
<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="co">## Download the archive from the RSAT distribution site</span></a>
<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="bu">export</span> <span class="va">DOWNLOAD_BASE=</span>http://pedagogix-tagc.univ-mrs.fr/download_rsat</a>
<a class="sourceLine" id="cb1-11" data-line-number="11"><span class="bu">export</span> <span class="va">RSAT_TGZ=</span>rsat_<span class="va">${RELEASE}</span>.tar.gz</a>
<a class="sourceLine" id="cb1-12" data-line-number="12"><span class="bu">export</span> <span class="va">DOWNLOAD_URL=${DOWNLOAD_BASE}</span>/<span class="va">${RSAT_TGZ}</span></a>
<a class="sourceLine" id="cb1-13" data-line-number="13"><span class="bu">echo</span> <span class="st">"Downloading RSAT from URL\t</span><span class="va">${DOWNLOAD_URL}</span><span class="st">"</span></a>
<a class="sourceLine" id="cb1-14" data-line-number="14"><span class="fu">wget</span> --no-clobber <span class="va">${DOWNLOAD_URL}</span></a>
<a class="sourceLine" id="cb1-15" data-line-number="15"><span class="fu">tar</span> -C <span class="va">${INSTALL_ROOT}</span>/ -xpvzf <span class="va">${RSAT_TGZ}</span></a>
<a class="sourceLine" id="cb1-16" data-line-number="16"><span class="bu">cd</span> <span class="va">${INSTALL_ROOT}</span>/rsat</a></code></pre></div>
<hr />
</div>
</div>
<div id="configuring-your-local-rsat-instance" class="section level1">
<h1><span class="header-section-number">4</span> Configuring your local RSAT instance</h1>
<p>We will start by auto-configuring RSAT in order to deine suitable basic parameters.</p>
<div id="getting-the-ip-address-of-your-machine" class="section level2">
<h2><span class="header-section-number">4.1</span> Getting the IP address of your machine</h2>
<p>Replace [your.server.IP] by the actual IP address of your server. (e.g.: for Virtualbox Virtual Machines, we set the IP to 192.168.56.101).</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="co">## Get your IP address</span></a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="ex">ifconfig</span> <span class="kw">|</span> <span class="fu">grep</span> <span class="st">'inet '</span></a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="bu">export</span> <span class="va">MY_IP=</span>XXX.XXX.XXX.XXX</a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co">## e.g. export MY_IP=192.168.56.101</span></a></code></pre></div>
<p>Note: if you install RSAT on a personal PC (e.g. a laptop) and intend to use it only from this machine, you can configure it with the local network.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co">## Configure RSAT to be used internally inly</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2">export MY_IP=<span class="dv">127</span>.<span class="dv">0</span>.<span class="fl">0.1</span></a></code></pre></div>
</div>
<div id="choose-a-site-name-for-your-rsat-instance" class="section level2">
<h2><span class="header-section-number">4.2</span> Choose a site name for your RSAT instance</h2>
<p>You can choose an arbitrary name for your RSAT instance. For this tutorial, we will call it <code>my_rsat</code>, but you are welcome to use another site name.</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="bu">export</span> <span class="va">RSAT_SITE=</span>my_rsat</a></code></pre></div>
</div>
<div id="automatic-configuration-of-rsat-parameters" class="section level2">
<h2><span class="header-section-number">4.3</span> Automatic configuration of RSAT parameters</h2>
<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb5-1" data-line-number="1"></a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co">## Check that the IP site of your machine has been specified</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="bu">export</span> <span class="va">RSAT=${INSTALL_ROOT}</span>/rsat</a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="bu">echo</span> <span class="st">"RSAT </span><span class="va">${RSAT}</span><span class="st">"</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"></a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co">## Check that the IP site of your machine has been specified</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="bu">echo</span> <span class="st">"MY_IP </span><span class="va">${MY_IP}</span><span class="st">"</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co">## Check that you defined a site name for your RSAT instance</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="bu">echo</span> <span class="st">"RSAT_SITE </span><span class="va">${RSAT_SITE}</span><span class="st">"</span></a>
<a class="sourceLine" id="cb5-11" data-line-number="11"></a>
<a class="sourceLine" id="cb5-12" data-line-number="12"><span class="co">## Semi-auto configuration for VirtualBox VM</span></a>
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co">## (adapt IP address if required)</span></a>
<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="fu">perl</span> perl-scripts/configure_rsat.pl -auto \</a>
<a class="sourceLine" id="cb5-15" data-line-number="15"> rsat=<span class="va">${RSAT}</span> \</a>
<a class="sourceLine" id="cb5-16" data-line-number="16"> rsat_site=<span class="va">${RSAT_SITE}</span> \</a>
<a class="sourceLine" id="cb5-17" data-line-number="17"> rsat_www=http://<span class="va">${MY_IP}</span>/rsat/ \</a>
<a class="sourceLine" id="cb5-18" data-line-number="18"> rsat_ws=http://<span class="va">${MY_IP}</span>/rsat/ \</a>
<a class="sourceLine" id="cb5-19" data-line-number="19"> ucsc_tools=1 \</a>
<a class="sourceLine" id="cb5-20" data-line-number="20"> ensembl_tools=1</a></code></pre></div>
<p>You can add some additional options to the previous command, e.g. enter your mail address as server admin, activate some specific tools that are disabled by default.</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="va">rsat_server_admin=</span>your.mail<span class="ex">@your.mail.server</span></a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="va">variation_tools=</span>1</a></code></pre></div>
<!--
## For the IFB cloud
RSAT has been ported on the cloud of the [**Institut Français de Bioinformatique**](http://www.france-bioinformatique.fr) (**IFB**). The tools are available as an appliance which enables each user to automatically start an RSAT server, that can be used in a terminal, via a Web interface, or invoked remotely as Web services.
Since the IP address is allocated dynamically during at the start of the instance booting, we use an automatic configuration.
```bash
perl perl-scripts/configure_rsat.pl -auto \
rsat_site=rsatvm-ifb-2018-05 \
RSAT=${INSTALL_ROOT}/rsat \
rsat_www=auto \
rsat_ws=auto \
phylo_tools=0 \
compara_tools=0 \
variations_tools=0 \
ucsc_tools=0 \
ensembl_tools=0 \
SUDO=sudo
chmod 755 /root # required for apache user to access the packages
```
-->
</div>
<div id="advanced-rsat-configuration" class="section level2">
<h2><span class="header-section-number">4.4</span> Advanced RSAT configuration</h2>
<p>In order to see all options, you can run the script <code>configure_rsat.pl</code> without the option <code>--auto</code></p>
<div class="sourceCode" id="cb7"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="fu">perl</span> perl-scripts/configure_rsat.pl</a></code></pre></div>
<p>You can now refine the configuration by choosing custom parameter to your RSAT instance (for example the email of the local admin, the organism group, …).</p>
<hr />
</div>
</div>
<div id="installing-rsat" class="section level1">
<h1><span class="header-section-number">5</span> Installing RSAT</h1>
<p>Before running the installation, it might be worth updating the Linux distribution (<code>apt-get update</code>) in order to get the latest versions of the basic packages.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="co">## This requires admin privileges</span></a>
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="fu">sudo</span> bash</a>
<a class="sourceLine" id="cb8-3" data-line-number="3"></a>
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="co">## Check who you are (should be root)</span></a>
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="fu">whoami</span></a>
<a class="sourceLine" id="cb8-6" data-line-number="6"></a>
<a class="sourceLine" id="cb8-7" data-line-number="7"><span class="co">## Define your operating system (currently supported: ubuntu, macosx) by running one (and only one) of the commands below. </span></a>
<a class="sourceLine" id="cb8-8" data-line-number="8"><span class="bu">export</span> <span class="va">MY_OS=</span>macosx</a>
<a class="sourceLine" id="cb8-9" data-line-number="9"><span class="bu">export</span> <span class="va">MY_OS=</span>ubuntu</a>
<a class="sourceLine" id="cb8-10" data-line-number="10"></a>
<a class="sourceLine" id="cb8-11" data-line-number="11"></a>
<a class="sourceLine" id="cb8-12" data-line-number="12"><span class="co">## Go to the RSAT directory</span></a>
<a class="sourceLine" id="cb8-13" data-line-number="13"><span class="bu">export</span> <span class="va">INSTALL_ROOT=</span>~/packages</a>
<a class="sourceLine" id="cb8-14" data-line-number="14"><span class="bu">cd</span> <span class="va">${INSTALL_ROOT}</span>/rsat</a>
<a class="sourceLine" id="cb8-15" data-line-number="15"></a>
<a class="sourceLine" id="cb8-16" data-line-number="16"><span class="co">## Read config and run bash installation scripts</span></a>
<a class="sourceLine" id="cb8-17" data-line-number="17"><span class="bu">source</span> RSAT_config.bashrc <span class="kw">&&</span> <span class="ex">\ </span></a>
<a class="sourceLine" id="cb8-18" data-line-number="18"><span class="fu">bash</span> installer/01_<span class="va">${MY_OS}</span>_packages.bash <span class="kw">&&</span> <span class="kw">\</span></a>
<a class="sourceLine" id="cb8-19" data-line-number="19"><span class="fu">bash</span> installer/02_python_packages.bash <span class="kw">&&</span> <span class="kw">\</span></a>
<a class="sourceLine" id="cb8-20" data-line-number="20"><span class="fu">bash</span> installer/03_install_rsat.bash <span class="kw">&&</span> <span class="kw">\</span></a>
<a class="sourceLine" id="cb8-21" data-line-number="21"><span class="fu">bash</span> installer/04_perl_packages.bash <span class="kw">&&</span> <span class="kw">\</span></a>
<a class="sourceLine" id="cb8-22" data-line-number="22"><span class="fu">bash</span> installer/06_install_organisms.bash <span class="kw">&&</span> <span class="kw">\</span></a>
<a class="sourceLine" id="cb8-23" data-line-number="23"><span class="fu">bash</span> installer/07_R-and-packages.bash <span class="kw">&&</span> <span class="kw">\</span></a>
<a class="sourceLine" id="cb8-24" data-line-number="24"><span class="fu">bash</span> installer/08_apache_config.bash <span class="kw">&&</span> <span class="kw">\</span></a>
<a class="sourceLine" id="cb8-25" data-line-number="25"><span class="fu">bash</span> installer/09_rsat_ws.bash <span class="kw">&&</span> <span class="kw">\</span></a>
<a class="sourceLine" id="cb8-26" data-line-number="26"><span class="fu">bash</span> installer/10_clean_unnecessary_files.bash</a>
<a class="sourceLine" id="cb8-27" data-line-number="27"></a>
<a class="sourceLine" id="cb8-28" data-line-number="28"><span class="co">## Restore rsat as owner of the $RSAT folder</span></a>
<a class="sourceLine" id="cb8-29" data-line-number="29"><span class="co">## </span><span class="al">NOTE</span><span class="co">: the following command should be adapted to the login and group of the user owing the rsat package.</span></a>
<a class="sourceLine" id="cb8-30" data-line-number="30"><span class="fu">chown</span> -R rsat.rsat <span class="va">$RSAT</span></a>
<a class="sourceLine" id="cb8-31" data-line-number="31"></a>
<a class="sourceLine" id="cb8-32" data-line-number="32"><span class="co">## Exit sudo session</span></a>
<a class="sourceLine" id="cb8-33" data-line-number="33"><span class="bu">exit</span></a>
<a class="sourceLine" id="cb8-34" data-line-number="34"></a>
<a class="sourceLine" id="cb8-35" data-line-number="35"><span class="co">## Check who you are (should be back to normal user identity)</span></a>
<a class="sourceLine" id="cb8-36" data-line-number="36"><span class="fu">whoami</span> <span class="co">## This should give 'rsat'</span></a></code></pre></div>
<hr />
</div>
<div id="testing-the-command-lines" class="section level1">
<h1><span class="header-section-number">6</span> Testing the command lines</h1>
<p>The script <code>makefile/install_tests.mk</code> runs a series of tests for different components of the <em>RSAT</em> suite. Each test result is stored in a separate file in the test directory (<code>./install_tests</code> by default). Output file names are printed out after each test.</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="co">## Load the RSAT configuration</span></a>
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="bu">source</span> RSAT_config.bashrc</a>
<a class="sourceLine" id="cb9-3" data-line-number="3"></a>
<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="bu">cd</span> <span class="va">$RSAT</span></a>
<a class="sourceLine" id="cb9-5" data-line-number="5"><span class="fu">make</span> -f makefiles/install_tests.mk all</a>
<a class="sourceLine" id="cb9-6" data-line-number="6"></a>
<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="co">## Check the results</span></a>
<a class="sourceLine" id="cb9-8" data-line-number="8"><span class="fu">ls</span> -ltr install_tests</a></code></pre></div>
<hr />
</div>
<div id="testing-the-web-server" class="section level1">
<h1><span class="header-section-number">7</span> Testing the Web server</h1>
<p>The RSAT Web site can be found at your host IP address followed by rsat: <a href="http://%5Bmy.computer.ip.address%5D/rsat/" class="uri">http://[my.computer.ip.address]/rsat/</a></p>
<p>e.g. for VirtualBox VM: <a href="http://192.168.56.101/rsat/" class="uri">http://192.168.56.101/rsat/</a></p>
<p>The web site can be tested by selecting any supported tool, clicking on the demo button and checking the result.</p>
<p>We usually use the following tools as diagnostic of the proper functioning of a server.</p>
<ol style="list-style-type: decimal">
<li><p><strong>Supported organisms</strong> to check if the default organisms have been installed.</p></li>
<li><p><strong>Fetch sequences from UCSC</strong>:</p>
<ul>
<li>is the list of organisms is correctly displayed (obtained dynamically from UCSC) ?</li>
<li>run the demo: do you obtain fasta sequences ?</li>
</ul></li>
<li><p><strong>retrieven Ensembl seq</strong>:</p>
<ul>
<li>is the list of organisms is correctly displayed (obtained dynamically from Ensembl) ?</li>
<li>run the demo 1 (single organism): do you obtain fasta sequences ?</li>
</ul></li>
<li><p><strong>convert-matrix</strong>: check that logos are properly generated</p></li>
<li><p><strong>gene-info</strong> to <strong>feature-map</strong>: check that the genes are well returned with gene-info, then successively send the results throught the following tools:</p>
<ul>
<li><p><strong>gene-info</strong> demo -> gene list. Check if you obtain a table with genes. If so, under <em>Next steps</em>, click the button <em>retrieve sequences</em>.</p></li>
<li><p><strong>retrieve sequences</strong>. Click “Run Analysis” then “GO”. In the result, check the fasta file. Next step: <em>oligo-analysis</em>.</p></li>
<li><p><strong>oligo-analysis</strong>. In the result, check the k-mers (oligos) then the matrices and the logos. In the Next step box, end the result to <em>string-based pattern matching</em>.</p></li>
<li><p><strong>dna-pattern</strong></p></li>
<li><p><strong>feature-map</strong> check that the png figure is properly generated and displayed.</p></li>
</ul></li>
</ol>
<p>At the end of this process the results should look like the figure below.</p>
<div class="figure" style="text-align: center">
<img src="images/feature-map_web_result.png" alt="**Feature-map result** at the end of the pipeline from *gene-info* to *feature-map*." width="60%" />
<p class="caption">
<strong>Feature-map result</strong> at the end of the pipeline from <em>gene-info</em> to <em>feature-map</em>.
</p>
</div>
</div>
<div id="testing-the-web-services" class="section level1">
<h1><span class="header-section-number">8</span> Testing the Web services</h1>
<div id="soapwsdl-interface" class="section level2">
<h2><span class="header-section-number">8.1</span> SOAP/WSDL interface</h2>
</div>
<div id="rest-interface" class="section level2">
<h2><span class="header-section-number">8.2</span> REST interface</h2>
<!-- **************************************************************** -->
<!-- # Supplementary information -->
<!-- ## Files -->
<!-- Stand-alone version + web servers for RSAT -->
<!-- `rsat_YYYY.MM.DD.tar.gz` -->
<!-- Metabolic pathway analysis tools (previously supported on the NeAT server, not maintained anymore). -->
<!-- `metabolic-tools_YYYYMMDD.tar.gz` -->
<!-- ## RSAT installation and user guides -->
<!-- After having uncompressed the archive, you will find the installation and user guides in the `doc/manuals` directory -->
<!-- ```{bash} -->
<!-- ls -1 public_html/release/*.pdf -->
<!-- ``` -->
<!-- | Guide | File | -->
<!-- |------------------------|---------------------------| -->
<!-- | RSAT installation guide | RSAT_install_guide.pdf | -->
<!-- | RSAT Web configuration guide | rsat_web_server.pdf | -->
<!-- | RSAT Command-linde user guide | tutorial_shell_rsat.pdf | -->
<!-- | NeAT Web server configuration | neat_web_server.pdf | -->
<!-- | NeAT Command-line user guide | neat_tutorial.pdf | -->
<!-- **************************************************************** -->
<!-- Define an environment variable specifying the path of RSAT directory -->
<!-- ```{bash} -->
<!-- ## Go th the main RSAT directory -->
<!-- cd ${RSAT} -->
<!-- ## Parameters to change -->
<!-- ## rsat_site rsat-vm-2016-03 -->
<!-- ## rsat_server_admin I don't specify it, because I don't want to receive notifications from all the VMs -->
<!-- ## I activate the optional tools ucsc_tools and ensembl_tools, but not the other ones because they require many genomes (phylo tools) or big genomes (compara_tools, variation_tools). -->
<!-- ## Load the (updated) RSAT environment variables -->
<!-- cd ${RSAT}; source RSAT_config.bashrc -->
<!-- ## Check that the RSAT environment variable has been properly -->
<!-- ## configured. Note: I also define it in the beginning of the script -->
<!-- ## because I will beed it for the different installation chunks. -->
<!-- echo "RSAT path: ${RSAT}" -->
<!-- cd ${RSAT} -->
<!-- ## Initialise RSAT folders -->
<!-- make -f makefiles/init_rsat.mk init -->
<!-- ################################################################ -->
<!-- ## Next steps require to be done as rsat administrator user -->
<!-- ## compile RSAT programs written in C -->
<!-- cd ${RSAT} -->
<!-- make -f makefiles/init_rsat.mk compile_all -->
<!-- df -m > ${RSAT}/install_logs/df_$(date +%Y-%m-%d_%H-%M-%S)_rsat_app_compiled.txt -->
<!-- ## !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -->
<!-- ## !!!!!!!!!!!!!!!!!!!!!!!!!!! BUG !!!!!!!!!!!!!!!!!!!!!!!!!!!! -->
<!-- ## !!!! I HAVE A PROBLEM TO COMPILE KWALKS. SHOULD BE CHECKED !!!!! -->
<!-- ## !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -->
<!-- ################################################################ -->
<!-- ## Install some third-party programs required by some RSAT scripts. -->
<!-- cd ${RSAT} -->
<!-- make -f makefiles/install_software.mk list_ext_apps -->
<!-- make -f makefiles/install_software.mk install_ext_apps -->
<!-- df -m > ${RSAT}/install_logs/df_$(date +%Y-%m-%d_%H-%M-%S)_rsat_extapp_installed.txt -->
<!-- ``` -->
<!-- # Dependencies -->
<!-- ## mkvtree and vmatch -->
<!-- The RSAT program `purge-sequences` is used to mask redundant sequences, which is strongly recommended before running motif discovery, since the over-representation statistics rely on the hypothesis of independence. -->
<!-- This perl script relies on the tools `mkvtree` and `vmatch` developed by Stefan Kurtz. -->
<!-- ```{bash eval=FALSE} -->
<!-- cd ${RSAT} -->
<!-- ## List dependencies for external applications -->
<!-- make -f makefiles/install_software.mk list_ext_apps -->
<!-- ## Install -->
<!-- make -f makefiles/install_software.mk install_vmatch -->
<!-- ``` -->
</div>
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