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<div id="header">
<h1 class="title toc-ignore">Installing genomes from Ensembl
Genomes</h1>
<h4 class="author">Bruno Contreras Moreira</h4>
<h4 class="date">2024-04-24</h4>
</div>
<div id="introduction" class="section level1" number="1">
<h1><span class="header-section-number">1</span> Introduction</h1>
<p>This document explains how to install genomes and annotations from
Ensembl Genomes using mostly the <a
href="ftp://ftp.ensemblgenomes.org/pub">FTP</a> site. Gene Ontology
terms are optional and are obtained from <a
href="http://plants.ensembl.org/biomart/martview">BioMart</a>
instead.</p>
<p>Note that while Ensembl covers Vertebrates, Ensembl Genomes (EG, also
known as Non Vertebrates, NV) includes the other divisions (Protists,
Fungi, Plants, Bacteria, Metazoa). These instructions have mostly been
tested with <strong>Ensembl Plants</strong>.</p>
<p>This protocol uses the Makefile <a
href="https://github.com/rsa-tools/rsat-code/blob/master/makefiles/ensemblgenomes_FTP_client.mk">ensemblgenomes_FTP_client.mk</a>,
which can also be used to install arbitrary genomes from other sources
from FASTA and GTF files, as explained in <a
href="https://rsa-tools.github.io/managing-RSAT/genome_installation/install_organisms_FASTA_GTF.html">Installing
organisms from FASTA and GTF files</a>.</p>
<p>This document <strong>does not</strong> use the following scripts,
which are documented in <a
href="https://rsa-tools.github.io/managing-RSAT/genome_installation/install_organisms_from_ensembl.html">Installing
genomes and variations from Ensembl</a>:</p>
<ul>
<li><code>install-ensembl-genome</code>,</li>
<li><code>download-ensembl-genome</code>,</li>
<li><code>download-ensembl-features</code>,</li>
<li><code>download-ensembl-variations</code>.</li>
</ul>
</div>
<div
id="installing-genome-sequences-and-annotations-from-ensembl-genomes"
class="section level1" number="2">
<h1><span class="header-section-number">2</span> Installing genome
sequences and annotations from Ensembl Genomes</h1>
<div id="check-ftp-site-url" class="section level2" number="2.1">
<h2><span class="header-section-number">2.1</span> Check FTP site
URL</h2>
<p>The current FTP site is at <a href="ftp://ftp.ensemblgenomes.org"
class="uri">ftp://ftp.ensemblgenomes.org</a> ; should it change in the
future, or its folder structure, <a
href="https://github.com/rsa-tools/rsat-code/blob/master/makefiles/ensemblgenomes_FTP_client.mk">ensemblgenomes_FTP_client.mk</a>
will be updated accordingly.</p>
</div>
<div id="find-out-current-ensembl-genomes-release"
class="section level2" number="2.2">
<h2><span class="header-section-number">2.2</span> Find out current
Ensembl Genomes release</h2>
<p>Visit the Web site of your division of interest, such as <a
href="http://plants.ensembl.org"
class="uri">http://plants.ensembl.org</a>, and check the release
statement at the bottom. Alternatively you can use the REST <a
href="http://rest.ensembl.org/documentation/info/eg_version">info/eg_version
endpoint</a></p>
<p>Ensembl Genome releases are integers and have an offset of 53 with
Ensembl releases. For instance, Ensembl release 99 corresponds to
Ensembl Genomes 46.</p>
<div class="sourceCode" id="cb1"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="bu">export</span> <span class="va">EGRELEASE</span><span class="op">=</span>46</span></code></pre></div>
</div>
<div id="get-supported-species" class="section level2" number="2.3">
<h2><span class="header-section-number">2.3</span> Get supported
species</h2>
<p>We shall download the current list of supported genomes in the
respective division (GROUP). This can be done by running the following
command:</p>
<div class="sourceCode" id="cb2"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$RSAT</span></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="bu">export</span> <span class="va">EGDIVISION</span><span class="op">=</span>Plants</span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a></span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=<span class="va">$EGRELEASE</span> organisms</span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a></span>
<span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a><span class="co"># in the example, this will create $RSAT/data/ensemblgenomes/plants/release-46/species_EnsemblPlants.txt</span></span></code></pre></div>
<p>Once this is done then you can install genomes from that release.</p>
</div>
</div>
<div id="install-all-species" class="section level1" number="3">
<h1><span class="header-section-number">3</span> Install all
species</h1>
<p>You can install all genomes with these commands:</p>
<div class="sourceCode" id="cb3"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$RSAT</span></span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a></span>
<span id="cb3-3"><a href="#cb3-3" tabindex="-1"></a><span class="co"># download FASTA and GTF files</span></span>
<span id="cb3-4"><a href="#cb3-4" tabindex="-1"></a><span class="fu">nohup</span> make <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=<span class="va">$EGRELEASE</span> download_all_species</span>
<span id="cb3-5"><a href="#cb3-5" tabindex="-1"></a></span>
<span id="cb3-6"><a href="#cb3-6" tabindex="-1"></a><span class="co"># parse input files, extract genomic features and compute oligo frequencies</span></span>
<span id="cb3-7"><a href="#cb3-7" tabindex="-1"></a><span class="fu">nohup</span> make <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=<span class="va">$EGRELEASE</span> install_all_species</span>
<span id="cb3-8"><a href="#cb3-8" tabindex="-1"></a></span>
<span id="cb3-9"><a href="#cb3-9" tabindex="-1"></a><span class="co"># check upstream sequences can be retrieved</span></span>
<span id="cb3-10"><a href="#cb3-10" tabindex="-1"></a><span class="fu">nohup</span> make <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=<span class="va">$EGRELEASE</span> check_all_species</span></code></pre></div>
<p>The newly installed species will be added to
$RSAT/data/supported_organisms.tab and should be listed with the
following command-line:</p>
<div class="sourceCode" id="cb4"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="ex">supported-organisms</span></span></code></pre></div>
<p>This will take a very long time, many days for a complete Ensembl
Genomes release. The most time-consuming task is the calculation of
genomic frequencies of oligos and dyads. Check the table for the
installation time of selected plant genomes:</p>
<table>
<thead>
<tr class="header">
<th align="left">organisms</th>
<th align="right">genome assembly length (Mb)</th>
<th align="right">installation time (minutes)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">Arabidopsis_thaliana.TAIR10.46</td>
<td align="right">119.7</td>
<td align="right">144</td>
</tr>
<tr class="even">
<td
align="left">Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46</td>
<td align="right">271.2</td>
<td align="right">233</td>
</tr>
<tr class="odd">
<td align="left">Oryza_sativa.IRGSP-1.0.46</td>
<td align="right">375.0</td>
<td align="right">290</td>
</tr>
<tr class="even">
<td align="left">Beta_vulgaris.RefBeet-1.2.2.46</td>
<td align="right">566.2</td>
<td align="right">320</td>
</tr>
<tr class="odd">
<td align="left">Glycine_max.Glycine_max_v2.1.46</td>
<td align="right">978.5</td>
<td align="right">660</td>
</tr>
<tr class="even">
<td align="left">Zea_mays.Zm-B73-REFERENCE-NAM-5.0.51</td>
<td align="right">2182.1</td>
<td align="right">1069</td>
</tr>
<tr class="odd">
<td align="left">Helianthus_annuus.HanXRQr1.0.46</td>
<td align="right">3027.8</td>
<td align="right">1689</td>
</tr>
<tr class="even">
<td align="left">Hordeum_vulgare.IBSCv2.46</td>
<td align="right">4834.4</td>
<td align="right">3574</td>
</tr>
<tr class="odd">
<td align="left">Triticum_aestivum.IWGSC.46</td>
<td align="right">14547.3</td>
<td align="right">10458</td>
</tr>
</tbody>
</table>
</div>
<div id="install-selected-species" class="section level1" number="4">
<h1><span class="header-section-number">4</span> Install selected
species</h1>
<p>In case you want to install a single genome you can do that by:</p>
<div class="sourceCode" id="cb5"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$RSAT</span></span>
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=<span class="va">$EGRELEASE</span> SPECIES=oryza_longistaminata download_one_species</span>
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=<span class="va">$EGRELEASE</span> SPECIES=oryza_longistaminata install_one_species</span></code></pre></div>
<p>You can also install selected genomes from older releases:</p>
<div class="sourceCode" id="cb6"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$RSAT</span></span>
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=42 organisms</span>
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=42 SPECIES=oryza_sativa download_one_species</span>
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=42 SPECIES=oryza_sativa install_one_species</span></code></pre></div>
<p>As indicated earlier, the newly installed species are added to
$RSAT/data/supported_organisms.tab and should appear in the list
produced by:</p>
<div class="sourceCode" id="cb7"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="ex">supported-organisms</span></span></code></pre></div>
</div>
<div id="other-optional-tasks" class="section level1" number="5">
<h1><span class="header-section-number">5</span> Other optional
tasks</h1>
<div id="compute-genome-stats-report" class="section level2"
number="5.1">
<h2><span class="header-section-number">5.1</span> Compute genome stats
report</h2>
<p>This step generates a report of descriptive stats of genomes
currently in your system, such as <a
href="http://rsat.eead.csic.es/plants/data/stats"
class="uri">http://rsat.eead.csic.es/plants/data/stats</a> :</p>
<div class="sourceCode" id="cb8"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk calc_stats</span></code></pre></div>
</div>
<div id="install-variation-data" class="section level2" number="5.2">
<h2><span class="header-section-number">5.2</span> Install variation
data</h2>
<p>If variation data is available for your species of interest you can
download it with:</p>
<div class="sourceCode" id="cb9"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$RSAT</span></span>
<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=<span class="va">$EGRELEASE</span> SPECIES=oryza_sativa variations_one_species</span></code></pre></div>
<p><strong>Note:</strong> this will update file
$RSAT/data/supported_organisms.tab</p>
</div>
<div id="download-and-install-ensembl-compara-homologies-optional"
class="section level2" number="5.3">
<h2><span class="header-section-number">5.3</span> Download and install
Ensembl Compara homologies (optional)</h2>
<p>Script <code>get-orthologs-compara</code> can be used to retrieve
homologues (orthologues by default) precomputed at Ensembl Compara. In
order to use it you must first install Compara in your system, which you
can do with:</p>
<div class="sourceCode" id="cb10"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$RSAT</span></span>
<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a><span class="bu">export</span> <span class="va">ENSRELEASE</span><span class="op">=</span>99</span>
<span id="cb10-3"><a href="#cb10-3" tabindex="-1"></a></span>
<span id="cb10-4"><a href="#cb10-4" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk RELEASE=<span class="va">$EGRELEASE</span> ENSEMBL_RELEASE=<span class="va">$ENSRELEASE</span> GROUP=<span class="va">$EGDIVISION</span> download_compara</span>
<span id="cb10-5"><a href="#cb10-5" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk RELEASE=<span class="va">$EGRELEASE</span> ENSEMBL_RELEASE=<span class="va">$ENSRELEASE</span> GROUP=<span class="va">$EGDIVISION</span> parse_compara_match</span>
<span id="cb10-6"><a href="#cb10-6" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk RELEASE=<span class="va">$EGRELEASE</span> ENSEMBL_RELEASE=<span class="va">$ENSRELEASE</span> GROUP=<span class="va">$EGDIVISION</span> install_compara</span></code></pre></div>
<p>All going well you can check the species with installed homologies
with:</p>
<div class="sourceCode" id="cb11"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a><span class="ex">get-orthologs-compara</span> <span class="at">-supported_organisms</span></span></code></pre></div>
</div>
<div id="install-gene-ontology-terms-from-biomart"
class="section level2" number="5.4">
<h2><span class="header-section-number">5.4</span> Install Gene Ontology
terms from BioMart</h2>
<p>These operations have been tested in Ensembl Plants, but should work
also with Metazoa and Fungi. They require the installation of optional
software, which can be done as follows:</p>
<div class="sourceCode" id="cb12"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="fu">sudo</span> bash</span>
<span id="cb12-2"><a href="#cb12-2" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$RSAT</span></span>
<span id="cb12-3"><a href="#cb12-3" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/install_software.mk install_biomart-perl check_biomart-perl</span></code></pre></div>
<p>To complete the configuration we shall get the current registry for
the division of interest. For instance, for Plants the registry is at <a
href="http://plants.ensembl.org/biomart/martservice?type=registry"
class="uri">http://plants.ensembl.org/biomart/martservice?type=registry</a></p>
<p>The XML content of the registry must be copied and pasted into file
<em>$RSAT/ext_lib/biomart-perl/conf/martURLLocation.xml</em> . For
instance, for Plants release 46 it looked like this:</p>
<pre><code><?xml version="1.0" encoding="UTF-8"?>
<MartRegistry>
<MartURLLocation database="plants_mart_46" default="" displayName="Ensembl Plants Genes 46" host="plants.ensembl.org" includeDatasets="" martUser="" name="plants_mart" path="/biomart/martservice" port="80" serverVirtualSchema="plants_mart" visible="1" />
<MartURLLocation database="plants_snp_mart_46" default="" displayName="Ensembl Plants Variations 46" host="plants.ensembl.org" includeDatasets="" martUser="" name="plants_variations" path="/biomart/martservice" port="80" serverVirtualSchema="plants_mart" visible="1" />
<MartURLLocation database="plants_sequence_mart_46" default="" displayName="Ensembl Plants Sequences 46" host="plants.ensembl.org" includeDatasets="" martUser="" name="plants_sequences" path="/biomart/martservice" port="80" serverVirtualSchema="plants_mart" visible="0" />
<MartURLLocation database="plants_genomic_features_mart_46" default="" displayName="Ensembl Plants Genomic Features 46" host="plants.ensembl.org" includeDatasets="" martUser="" name="plants_genomic_features" path="/biomart/martservice" port="80" serverVirtualSchema="plants_mart" visible="0" />
<MartURLLocation database="ontology_mart_99" default="" displayName="Ontology Mart 99" host="plants.ensembl.org" includeDatasets="" martUser="" name="ontology" path="/biomart/martservice" port="80" serverVirtualSchema="plants_mart" visible="0" />
</MartRegistry></code></pre>
<p>Once this is done we shall update the registry cache with:</p>
<div class="sourceCode" id="cb14"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a><span class="ex">download-ensembl-go-annotations-biomart</span> <span class="at">-reg</span></span></code></pre></div>
<p>This will take a few minutes, but then we can do:</p>
<div class="sourceCode" id="cb15"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb15-1"><a href="#cb15-1" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=<span class="va">$EGRELEASE</span> download_go</span></code></pre></div>
<p>And for each species for which we want GO terms we can now do:</p>
<div class="sourceCode" id="cb16"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb16-1"><a href="#cb16-1" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk GROUP=<span class="va">$EGDIVISION</span> RELEASE=<span class="va">$EGRELEASE</span> SPECIES=oryza_sativa download_go_annotations</span></code></pre></div>
<hr />
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