<div dir="ltr">Dear Matthew,<div><br></div><div>Thanks a lot for your response. I have submitted the same.</div><div><br></div><div>Thanks & Regards</div><div>Fazulur Rehaman</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 18, 2018 at 9:27 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 text="#000000" bgcolor="#FFFFFF">
Hello Fazulur,<br>
<br>
I just spoke with our web team who maintains that code and better
knows how to debug it. They requested you please submit a ticket
through our helpdesk [1] about this so they can better track the
responses and assist you with your issues. Thanks.<br>
<br>
[1] <a class="m_214156357339423287moz-txt-link-freetext" href="https://www.ensembl.org/info/about/contact/index.html" target="_blank">https://www.ensembl.org/info/<wbr>about/contact/index.html</a><div><div class="h5"><br>
<br>
<div class="m_214156357339423287moz-cite-prefix">On 18/01/18 15:49, Rehaman wrote:<br>
</div>
<blockquote type="cite">
<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" target="_blank">https://asia.ensembl.org/<wbr>info/docs/webcode/mirror/<wbr>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>
<div><br>
</div>
<div>Thanks & Regards</div>
<div>Fazulur Rehaman</div>
</span></div>
<div class="m_214156357339423287HOEnZb">
<div class="m_214156357339423287h5">
<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_214156357339423287m_6996420949288595663h5"><br>
<br>
<div class="m_214156357339423287m_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_214156357339423287m_6996420949288595663m_-3239872116264969872h5"><br>
<br>
<div class="m_214156357339423287m_6996420949288595663m_-3239872116264969872m_-1050681698239178095moz-cite-prefix">On
10/01/18 10:46, Rehaman
wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="m_214156357339423287m_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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