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    Hi Duarte,<br>
    <br>
    The VEP --assembly flag uses the solution I suggested initially,
    which is to have the two databases on two separate servers.<br>
    By specifying --assembly GRCh37, the default 3306 port is replaced
    by the 3337 port, which is where the GRCh37 databases are hosted.<br>
    It is worth noting as well that only the human databases on port
    3337 are updated, all the other databases are identical to the ones
    from release 75.<br>
    <br>
    The current implementation of the registry does not support two core
    databases for a single species on the same server.<br>
    <br>
    The solutions are:<br>
    - use two separate servers<br>
    In the case of our live servers, we have ensembldb.ensembl.org:3306
    for GRCh38 and ensembl.ensembl.org:3337 for GRCh37<br>
    - bypass the registry and specify each required database
    individually<br>
    This will only work if connecting to one database at a time<br>
    <br>
    Our system is currently in transition between two models.<br>
    Historically, one species has one assembly at one given time.<br>
    With the migration from GRCh37 to GRCh38 and the future of genomics,
    we see the need to support multiple assemblies for a single species.<br>
    We are currently working on better solutions for this.<br>
    <br>
    <br>
    Regards,<br>
    Magali<br>
    <br>
    <div class="moz-cite-prefix">On 28/04/2015 09:51, Duarte Molha
      wrote:<br>
    </div>
    <blockquote
cite="mid:CAGqkoELxsZj_PPevbFQhAS9TZuivSu2x0b0Jc8djffVuaVwEjw@mail.gmail.com"
      type="cite">
      <div dir="ltr">Ok ... thanks Magali.
        <div><br>
        </div>
        <div>I believe the latest VEP now supports an --assembly flag to
          allow it to annotate against a specific assembly.</div>
        <div>Can we not have the same flag on the registry ? </div>
        <div>How does VEP do it?</div>
        <div>This would be incredibly useful because I would not have to
           create new scripts to support a different assembly.<br>
        </div>
        <div><br>
        </div>
        <div>I could just download all the tables and just tell the
          registry which one to use.</div>
        <div><br>
        </div>
        <div>Please correct me if I am wrong but your proposed solution
          would mean I would have to bypass the registry completely and
          I would need to create each each adaptor from scratch and thus
          I would need to alter a lot of my scripts to support both
          assemblies.</div>
        <div><br>
        </div>
        <div>"--assembly GRCh37" would be a much more preferable route.</div>
        <div><br>
        </div>
        <div>Best regards,<br>
        </div>
        <div><br>
        </div>
        <div>    Duarte</div>
        <div><br>
        </div>
        <div><br>
        </div>
        <div><br>
        </div>
      </div>
      <div class="gmail_extra"><br clear="all">
        <div>
          <div class="gmail_signature"><font
              style="background-color:rgb(255,255,255)" color="#999999">=========================<br>
                   Duarte Miguel Paulo Molha      <br>
            </font>
            <div><font style="background-color:rgb(255,255,255)"
                color="#999999">         <a moz-do-not-send="true"
                  href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> 
                       <br>
                =========================</font></div>
          </div>
        </div>
        <br>
        <div class="gmail_quote">On 27 April 2015 at 17:48, mag <span
            dir="ltr"><<a moz-do-not-send="true"
              href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div bgcolor="#FFFFFF" text="#000000"> Hi Duarte,<br>
              <br>
              The mysql dumps for GRCh37 are available on the ftp site
              as well<br>
              <a moz-do-not-send="true"
                href="ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/"
                target="_blank">ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/</a><br>
              <br>
              I would recommend having only one copy of human for
              release 79.<br>
              So if you are interested in the GRCh37 data, you can
              download the database from <a moz-do-not-send="true"
                href="ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/"
                target="_blank">ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/</a>
              rather than <a moz-do-not-send="true"
                href="ftp://ftp.ensembl.org/pub/release-79/mysql/"
                target="_blank">ftp://ftp.ensembl.org/pub/release-79/mysql/</a><br>
              <br>
              If you need both databases on the same server, you can
              access a given database directly rather than using the
              registry.<br>
              my $human_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(<br>
                  -HOST => 'localhost',<br>
                  -PORT => 3306,<br>
                  -USER => 'user',<br>
                  -DBNAME => 'homo_sapiens_core_79_37',<br>
                  -SPECIES => 'homo_sapiens',<br>
                  -GROUP => 'core'<br>
              );<br>
              <br>
              <br>
              Hope that helps,<br>
              Magali<span class=""><br>
                <br>
                <div>On 27/04/2015 17:11, Duarte Molha wrote:<br>
                </div>
              </span>
              <blockquote type="cite">
                <div dir="ltr"><span class="">Thanks Magali
                    <div><br>
                    </div>
                    <div>But I think you have not understtod my
                      question.</div>
                    <div><br>
                    </div>
                    <div>Assume I want to download the databases to my
                      local computer and use the perl API 79 to query
                      the latest 79_37 database instead of the default
                      79_38<font size="3">. </font></div>
                    <div><font size="3">Previously, I just had to
                        download the mysql tables corresponding to the
                        api I was using to fetch the data correctly,
                        however, now you have broken that link
                        API->Underlying_assembly</font></div>
                    <div><font size="3"><br>
                      </font></div>
                    <div><font size="3">So how do I tell my scripts what
                        database to query?</font></div>
                    <div><font size="3"><br>
                      </font></div>
                    <div><font size="3">My local sql will all be under
                        the same port.</font></div>
                    <div><font size="3"><br>
                      </font></div>
                  </span>
                  <div><font size="3">Best regards</font></div>
                  <div><font size="3"><br>
                    </font></div>
                  <div><font size="3">Duarte</font></div>
                  <div><font size="3"><br>
                    </font></div>
                  <div><font size="3"><br>
                    </font></div>
                </div>
                <div class="gmail_extra"><span class=""><br clear="all">
                    <div>
                      <div><font
                          style="background-color:rgb(255,255,255)"
                          color="#999999">=========================<br>
                               Duarte Miguel Paulo Molha      <br>
                        </font>
                        <div><font
                            style="background-color:rgb(255,255,255)"
                            color="#999999">         <a
                              moz-do-not-send="true"
                              href="http://about.me/duarte"
                              target="_blank">http://about.me/duarte</a> 
                                   <br>
                            =========================</font></div>
                      </div>
                    </div>
                    <br>
                  </span>
                  <div class="gmail_quote"><span class="">On 27 April
                      2015 at 17:01, mag <span dir="ltr"><<a
                          moz-do-not-send="true"
                          href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
                      wrote:<br>
                    </span>
                    <div>
                      <div class="h5">
                        <blockquote class="gmail_quote" style="margin:0
                          0 0 .8ex;border-left:1px #ccc
                          solid;padding-left:1ex">
                          <div bgcolor="#FFFFFF" text="#000000"> Hi
                            Duarte,<br>
                            <br>
                            The archive 75 website is still based on the
                            release 75 API.<br>
                            <br>
                            For the dedicated GRCh37 website though, we
                            have used a data freeze from release 75 and
                            have since been updating the website and
                            underlying databases along with the main
                            release.<br>
                            The GRCh37 databases are available on our
                            main MySQL server on port 3337 (instead of
                            the default 3306 which will give you access
                            to GRCh38 databases)<br>
                            <br>
                            <br>
                            Hope that helps,<br>
                            Magali
                            <div>
                              <div><br>
                                <br>
                                <div>On 27/04/2015 16:56, Duarte Molha
                                  wrote:<br>
                                </div>
                              </div>
                            </div>
                            <blockquote type="cite">
                              <div>
                                <div>
                                  <div dir="ltr">
                                    <div>Dear developers</div>
                                    <div><br>
                                    </div>
                                    <div>On your GRCh37 archive site you
                                      say this:</div>
                                    <div><br>
                                    </div>
                                    <div>===========================</div>
                                    <div><br>
                                    </div>
                                    <h2>About this archive</h2>
                                    <p>This archive is based on Ensembl
                                      Release 75 data, and gives
                                      continuing access to human
                                      assembly GRCh37, as well as all
                                      our other release 75 species (data
                                      freeze March 2014) for comparative
                                      purposes. Human variation and
                                      regulation data has since been
                                      updated in March 2015.</p>
                                    <p>The API and website will be
                                      updated in tandem with the release
                                      of the main Ensembl website (<b>currently

                                        version 79</b>), and we will
                                      also periodically update this site
                                      with new data human, which will be
                                      announced in this panel.</p>
                                    <div><span>MySQL dumps of human
                                        databases on the most recent
                                        schema version are available on
                                        our</span><span> </span><a
                                        moz-do-not-send="true"
                                        href="ftp://ftp.ensembl.org/pub/grch37/"
                                        target="_blank">FTP site</a><span>.</span></div>
                                    <div><br>
                                    </div>
                                    <div>=========================</div>
                                    <div><br>
                                    </div>
                                    <div>It was my understanding that an
                                      API version was directly linked to
                                      a specific assembly. So I thought
                                      that if I wanted to query the
                                      latest GRCh37 assembly I would
                                      need to use the api v75 and if I
                                      wanted to use a local database, I
                                      would download the corresponding
                                      sql tables for that version.</div>
                                    <div><br>
                                    </div>
                                    <div>However, according to this
                                      announcement, I can now use the
                                      V79 api and query the old
                                      assembly... How is this
                                      accomplished ?</div>
                                    <div>What you I have to do on my
                                      scripts to make sure I am querying
                                      the 37 version even though I am
                                      using the latest API?</div>
                                    <div><br>
                                    </div>
                                    <div>Sorry, I hope this is not a
                                      stupid question but I am a bit
                                      confused.</div>
                                    <div><br>
                                    </div>
                                    <div>Best regards</div>
                                    <div><br>
                                    </div>
                                    <div>Duarte</div>
                                    <div><br>
                                    </div>
                                    <div><br>
                                    </div>
                                    <br clear="all">
                                    <div>
                                      <div><font
                                          style="background-color:rgb(255,255,255)"
                                          color="#999999">=========================<br>
                                               Duarte Miguel Paulo Molha
                                               <br>
                                        </font>
                                        <div><font
                                            style="background-color:rgb(255,255,255)"
                                            color="#999999">         <a
                                              moz-do-not-send="true"
                                              href="http://about.me/duarte"
                                              target="_blank">http://about.me/duarte</a> 
                                                   <br>
                                            =========================</font></div>
                                      </div>
                                    </div>
                                  </div>
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