<div dir="ltr">Hello,<div><br></div><div>The easiest way to do this would be to use the --custom option with VCF files representing the data you want to use. Both COSMIC and dbSNP provide VCF files that you can download and use in this way.</div><div><br></div><div>The custom data option also allows you to extract any arbitrary INFO field from the VCF should you require more information than just the location and/or identifier.</div><div><br></div><div>Due to changes in data access policy, Ensembl can only continue to distribute COSMIC v71. We do include new dbSNP builds as and when they are released, though there is a lag between its release and appearance in Ensembl/VEP. The latest version of VEP (82, released this week) includes dbSNP 144.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 30 September 2015 at 22:27, Davineni, Phani Kishore <span dir="ltr"><<a href="mailto:PDAVINENI@partners.org" target="_blank">PDAVINENI@partners.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I have a question regarding the data sources by VEP. Currently the cosmic version available through VEP is v71.<br>
Is it possible to make you different version of cosmic and dbSNP (in other words build/integrate these into your cache) regardless of what VEP pre built cache uses.I saw the option of --custom where you can use your datasets for annotation. Are there any other ways<br>
<br>
Example: VEP version 79,don't want to change the API, instead of cosmic v71 (use cosmic v74) and similar with dbSNP use v144/145 instead of 138 that comes with prebuilt cache.<br>
<br>
Thanks,<br>
Thanks in advance,<br>
<br>
Phani Kishore Davineni<br>
Bioinformatics Software Engineer,<br>
Center for Advanced Molecular Diagnostics,<br>
Brigham and Women's Hospital, Boston,MA 02115<br>
<br>
-----Original Message-----<br>
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Today's Topics:<br>
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1. Re: Configuring ensembl in a local system (Anne Lyle)<br>
2. Re: Problem attempting to install VEP 77 (Nicolas Thierry-Mieg)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 29 Sep 2015 16:30:41 +0100<br>
From: Anne Lyle <<a href="mailto:annelyle@ebi.ac.uk">annelyle@ebi.ac.uk</a>><br>
Subject: Re: [ensembl-dev] Configuring ensembl in a local system<br>
To: Ensembl dev list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID: <<a href="mailto:20C47C07-0D33-4680-B4DD-E176A09E6962@ebi.ac.uk">20C47C07-0D33-4680-B4DD-E176A09E6962@ebi.ac.uk</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Duarte<br>
<br>
I understand your frustrations, but we have a long long list of priorities and limited resources. As I stated, we are happy to help with individual installations, which is often the most practical solution since everyone?s setup is slightly different.<br>
<br>
Cheers<br>
<br>
Anne<br>
<br>
<br>
> On 29 Sep 2015, at 16:03, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br>
><br>
> Dear Anne<br>
><br>
> I share my frustration with Dadu. Yes it is a complex system but the instructions on your website are broken and incomplete and have been for a long long time!<br>
><br>
> I have given up for now on trying to install it because one of your colleagues said it would be refreshed soon and was in your list of priorities ... so far nothing.. for months!<br>
><br>
><br>
><br>
> Duarte Molha<br>
> <a href="http://about.me/duarte" rel="noreferrer" target="_blank">about.me/duarte</a><br>
><br>
> <<a href="https://about.me/duarte?promo=email_sig" rel="noreferrer" target="_blank">https://about.me/duarte?promo=email_sig</a>><br>
><br>
><br>
> On 29 September 2015 at 15:17, Anne Lyle <<a href="mailto:annelyle@ebi.ac.uk">annelyle@ebi.ac.uk</a> <mailto:<a href="mailto:annelyle@ebi.ac.uk">annelyle@ebi.ac.uk</a>>> wrote:<br>
> Hi Dadu<br>
><br>
> Sorry you?re having problems installing Ensembl - it is a very complex system and so the instructions are necessarily complicated, although we do try to make them as clear as possible. Please could you send any specific questions to <a href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a> <mailto:<a href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a>> and we will endeavour to guide you through the process - it would be helpful if you could provide an exact description of what you have done so far and any error messages produced by the server.<br>
><br>
> Cheers<br>
><br>
> Anne<br>
><br>
><br>
><br>
><br>
> Anne Lyle<br>
> Ensembl Web Developer<br>
> European Bioinformatics Institute (EMBL-EBI) East Wing, A3-118,<br>
> Wellcome Trust Genome Campus, Hinxton, Cambridge, UK<br>
><br>
> Phone: <a href="tel:%2B44%20%280%291223%20494178" value="+441223494178">+44 (0)1223 494178</a> <tel:%2B44%20%280%291223%20494178><br>
> Email: <a href="mailto:annelyle@ebi.ac.uk">annelyle@ebi.ac.uk</a> <mailto:<a href="mailto:annelyle@ebi.ac.uk">annelyle@ebi.ac.uk</a>><br>
> Web: <a href="http://www.ensembl.org" rel="noreferrer" target="_blank">www.ensembl.org</a> <<a href="http://www.ensembl.org/" rel="noreferrer" target="_blank">http://www.ensembl.org/</a>><br>
><br>
><br>
><br>
><br>
><br>
>> On 28 Sep 2015, at 07:37, Dadu <<a href="mailto:khalandardvg@gmail.com">khalandardvg@gmail.com</a> <mailto:<a href="mailto:khalandardvg@gmail.com">khalandardvg@gmail.com</a>>> wrote:<br>
>><br>
>> Dear All,<br>
>><br>
>> I am new to ensemble genome browser. I am trying configure ensemble in my local system for chickpea crop. I have followed below link to install and configure but I am unable to do it. I request you to provide easy steps to install and configuration of genome browser.<br>
>><br>
>> link:<br>
>> <a href="http://asia.ensembl.org/info/docs/webcode/mirror/install/index.html" rel="noreferrer" target="_blank">http://asia.ensembl.org/info/docs/webcode/mirror/install/index.html</a><br>
>> <<a href="http://asia.ensembl.org/info/docs/webcode/mirror/install/index.html" rel="noreferrer" target="_blank">http://asia.ensembl.org/info/docs/webcode/mirror/install/index.html</a>><br>
>><br>
>><br>
>> Thanks and regards,<br>
>> Dadakhalandar<br>
>> _______________________________________________<br>
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Message: 2<br>
Date: Tue, 29 Sep 2015 22:53:19 +0200<br>
From: Nicolas Thierry-Mieg <<a href="mailto:Nicolas.Thierry-Mieg@imag.fr">Nicolas.Thierry-Mieg@imag.fr</a>><br>
Subject: Re: [ensembl-dev] Problem attempting to install VEP 77<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID: <<a href="mailto:560AFA3F.1080901@imag.fr">560AFA3F.1080901@imag.fr</a>><br>
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<br>
Hi,<br>
<br>
works here on centos 6, but I avoid CPAN as much as possible and use the distro-provided perl-Archive-Extract-0.38-141.el6.x86_64 .<br>
<br>
HTH<br>
<br>
<br>
On 09/29/2015 05:23 PM, Murphy, David wrote:<br>
> Hi All<br>
><br>
> We?ve been trying to install VEP 77<br>
> (<a href="https://github.com/Ensembl/ensembl-tools/archive/release/77.zip" rel="noreferrer" target="_blank">https://github.com/Ensembl/ensembl-tools/archive/release/77.zip</a>) in<br>
> order to replicate results from a previous analysis.<br>
><br>
><br>
> We?re running perl v5.10.1 on Red Hat Enterprise Linux Server release<br>
> 6.6 (Santiago)<br>
><br>
> sh-4.1# perl -version<br>
><br>
> This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi<br>
><br>
><br>
> When we run Install.pl we get the error<br>
><br>
><br>
> sh-4.1# perl INSTALL.pl<br>
><br>
<snip><br>
> - unpacking ./Bio/tmp/ensembl.zip<br>
><br>
> Key 'archive' is of invalid type for Archive::Extract::new provided by<br>
> main::unpack_arch at /usr/share/perl5/Archive/Extract.pm line 270.<br>
><br>
> Can't call method "extract" on an undefined value at INSTALL.pl line 905.<br>
><br>
><br>
> The file ensembl.zip is downloaded and appears to be a valid zip<br>
> archive and can be extracted manually.<br>
><br>
> The perl core module Archive::Extract appears to be there.<br>
><br>
> Package namespace installed latest in CPAN file<br>
><br>
> Algorithm::Diff 1.1903 1.1903<br>
> TYEMQ/Algorithm-Diff-1.1903.tar.gz<br>
><br>
> App::cpanminus 1.7039 1.7039<br>
> MIYAGAWA/App-cpanminus-1.7039.tar.gz<br>
><br>
> Archive::Extract 0.74 0.76<br>
> BINGOS/Archive-Extract-0.76.tar.gz<br>
><br>
> Archive::Zip 1.51 1.53 PHRED/Archive-Zip-1.53.tar.gz<br>
><br>
> Attribute::Handlers 0.85 0.99<br>
> RJBS/Attribute-Handlers-0.99.tar.gz<br>
><br>
><br>
> We also tried with the latest version of the installer to try to<br>
> diagnose the problem but we got the same error.<br>
><br>
> Any ideas for what might be wrong?<br>
><br>
> Regards<br>
> David<br>
<br>
<br>
<br>
<br>
------------------------------<br>
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