<div dir="ltr"><div>Dear Matthew,</div><div><br></div><div>We have installed Ensembl server as per instructions (<a href="https://asia.ensembl.org/info/docs/webcode/mirror/index.html">https://asia.ensembl.org/info/docs/webcode/mirror/index.html</a>) and able to see ensembl webpage.</div><div><br></div><div>Homo sapiens data loaded to MySQL and updated .ini files as instructed. Created species specific ini files (homo_sapiens.ini) and added organism specific databases and restarted the server. When queried for BRCA2 under homo_sapiens it's giving error. We spend some time to debug and not succeeded. Please find attached screen shot of private server and error log.</div><div>Its related to ORM and few perl modules. All dependency modules including "Rose" were installed and exported perl5lib too. </div><div><br></div><div>Could you please suggest me how to resolve this.</div><div><br></div><div>Thanks in Advance</div><div>Fazulur Rehaman</div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Jan 14, 2018 at 5:47 PM, Rehaman <span dir="ltr"><<a href="mailto:ensemblfan@gmail.com" target="_blank">ensemblfan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Dear Matthew,</div><div><br></div><div>Thanks a lot for your answer.</div><div><br></div><div>We are still in installation process of private ensemble server. We will post if we have any further issues.</div><span class=""><div><br></div><div>Thanks & Regards</div><div>Fazulur Rehaman</div></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 12, 2018 at 4:14 PM, Matthew Laird <span dir="ltr"><<a href="mailto:lairdm@ebi.ac.uk" target="_blank">lairdm@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 Fazulur,<br>
<br>
I've raised the issue with the appropriate teams that yes we have
local installation instructions but we don't have release to release
upgrade instructions. To upgrade from one release to the next:<br>
<br>
- download and install the latest database versions of the species
you want in your local installation, as per the installation
instructions<br>
- for each of the ensembl* git repositories, in the directory for
that repository run: git fetch; git checkout release/91 (where you
replace the 91 with whichever new version in the future)<br>
- delete everything in the conf/packed directory for the web code<br>
- restart the web server, as per the installation instructions<br>
<br>
If you have any trouble with this, please let us know and we'll try
to assist you.<br>
<br>
Cheers.<div><div class="m_6996420949288595663h5"><br>
<br>
<div class="m_6996420949288595663m_-3239872116264969872moz-cite-prefix">On 11/01/18 06:47, Rehaman wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Dear Ensembl team,</div>
<div><br>
</div>
<div>Thanks a lot for quick response.</div>
<div><br>
</div>
<div>I have one more question.</div>
<div>Could you please let me know how to update our private
server for next Ensembl's release. </div>
<div><br>
</div>
<div>Thanks & Regards</div>
<div>Fazulur Rehaman</div>
<div><br>
</div>
<div>Thanks & Regards</div>
<div>Fazulur Rehaman</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jan 10, 2018 at 4:40 PM,
Matthew Laird <span dir="ltr"><<a href="mailto:lairdm@ebi.ac.uk" target="_blank">lairdm@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"> Hello Rehaman,<br>
<br>
Unfortunately I think you've misunderstood what the
installation instructions are trying to say. We no longer
recommend the local installation of BioMart as part of a
local mirror, and when the documentation says to link to a
public BioMart, it means to run your queries against a
public BioMart and Ensembl database. There isn't a way to
have our public BioMart instances talk to your private
server. If you need to do large queries against a local
Ensembl mirror, you're better off using the API in that
case.<br>
<br>
Please let us know if you have any further questions.
Cheers.
<div>
<div class="m_6996420949288595663m_-3239872116264969872h5"><br>
<br>
<div class="m_6996420949288595663m_-3239872116264969872m_-1050681698239178095moz-cite-prefix">On
10/01/18 10:46, Rehaman wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="m_6996420949288595663m_-3239872116264969872h5">
<div dir="ltr">
<div>Dear Team,</div>
<div><br>
</div>
<div>We are configuring Ensembl mirror locally in
our environment as per instructions.</div>
<div>Now we need to install BioMart. In
Documentation, It is saying that it is not
recommended to install.</div>
<div><br>
</div>
<div>Could you please let us know the process of
linking public BioMart.to ensembl local server?</div>
<div><br>
</div>
<div>Thanks in advance</div>
<div>Rehaman</div>
</div>
<br>
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