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Hi Rehaman<br>
<br>
We did not receive a request for you on helpdesk, so I'm not sure
what happened. I have just created a ticket for you, numbered
238614. You should get a reply to this soon.<br>
<br>
All the best<br>
<br>
Emily<br>
<br>
<div class="moz-cite-prefix">On 23/01/2018 04:20, Rehaman wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAOnJw47un-WhuhFAEAkkoPwy_JHbJgVxJD0Bir80O2uppbRKNQ@mail.gmail.com">
<div dir="ltr">
<div>Dear Matthew,</div>
<div><br>
</div>
<div>With respect to my previous question about errors on
Ensembl installation, I submitted to helpdesk, till now I
didn't get any response from them. I have given my mail ID (<a
href="mailto:vrehaman@gmail.com" moz-do-not-send="true">vrehaman@gmail.com</a>)
while submitting to help desk.</div>
<div><br>
</div>
<div>Could you please let me know the status and help me to
resolve the issue.</div>
<div><br>
</div>
<div>Thanks In Advance</div>
<div>Fazulur Rehaman</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Jan 19, 2018 at 7:50 AM,
Rehaman <span dir="ltr"><<a
href="mailto:ensemblfan@gmail.com" target="_blank"
moz-do-not-send="true">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">Dear Matthew,
<div><br>
</div>
<div>Thanks a lot for your response. I have submitted
the same.</div>
<span>
<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 Thu, Jan 18, 2018 at
9:27 PM, Matthew Laird <span dir="ltr"><<a
href="mailto:lairdm@ebi.ac.uk" target="_blank"
moz-do-not-send="true">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
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_7212080115334780557m_214156357339423287moz-txt-link-freetext"
href="https://www.ensembl.org/info/about/contact/index.html"
target="_blank" moz-do-not-send="true">https://www.ensembl.org/info/a<wbr>bout/contact/index.html</a>
<div>
<div class="m_7212080115334780557h5"><br>
<br>
<div
class="m_7212080115334780557m_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"
moz-do-not-send="true">https://asia.ensembl.org/info<wbr>/docs/webcode/mirror/index.<wbr>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"
moz-do-not-send="true">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_7212080115334780557m_214156357339423287HOEnZb">
<div
class="m_7212080115334780557m_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"
moz-do-not-send="true">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_7212080115334780557m_214156357339423287m_6996420949288595663h5"><br>
<br>
<div
class="m_7212080115334780557m_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" moz-do-not-send="true">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_7212080115334780557m_214156357339423287m_6996420949288595663m_-3239872116264969872h5"><br>
<br>
<div
class="m_7212080115334780557m_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_7212080115334780557m_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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Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
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<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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