[ensembl-dev] Updating dbSNP cosmic and ESP versions

Will McLaren wm2 at ebi.ac.uk
Thu Oct 1 09:36:18 BST 2015


Hello,

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.

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.

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.

Regards

Will McLaren
Ensembl Variation

On 30 September 2015 at 22:27, Davineni, Phani Kishore <
PDAVINENI at partners.org> wrote:

> Hi,
>
> I have a question regarding the data sources by VEP. Currently the cosmic
> version available through VEP is v71.
> 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
>
> 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.
>
> Thanks,
> Thanks in advance,
>
> Phani Kishore Davineni
> Bioinformatics Software Engineer,
> Center for Advanced Molecular Diagnostics,
> Brigham and Women's Hospital, Boston,MA 02115
>
> -----Original Message-----
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf
> Of dev-request at ensembl.org
> Sent: Wednesday, September 30, 2015 7:00 AM
> To: dev at ensembl.org
> Subject: Dev Digest, Vol 63, Issue 19
>
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> Today's Topics:
>
>    1. Re: Configuring ensembl in a local system (Anne Lyle)
>    2. Re: Problem attempting to install VEP 77 (Nicolas Thierry-Mieg)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 29 Sep 2015 16:30:41 +0100
> From: Anne Lyle <annelyle at ebi.ac.uk>
> Subject: Re: [ensembl-dev] Configuring ensembl in a local system
> To: Ensembl dev list <dev at ensembl.org>
> Message-ID: <20C47C07-0D33-4680-B4DD-E176A09E6962 at ebi.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Duarte
>
> 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.
>
> Cheers
>
> Anne
>
>
> > On 29 Sep 2015, at 16:03, Duarte Molha <duartemolha at gmail.com> wrote:
> >
> > Dear Anne
> >
> > 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!
> >
> > 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!
> >
> >
> >
> > Duarte Molha
> > about.me/duarte
> >
> >  <https://about.me/duarte?promo=email_sig>
> >
> >
> > On 29 September 2015 at 15:17, Anne Lyle <annelyle at ebi.ac.uk <mailto:
> annelyle at ebi.ac.uk>> wrote:
> > Hi Dadu
> >
> > 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 helpdesk at ensembl.org <mailto:helpdesk at ensembl.org> 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.
> >
> > Cheers
> >
> > Anne
> >
> >
> >
> >
> > Anne Lyle
> > Ensembl Web Developer
> > European Bioinformatics Institute (EMBL-EBI) East Wing, A3-118,
> > Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
> >
> > Phone: +44 (0)1223 494178 <tel:%2B44%20%280%291223%20494178>
> > Email: annelyle at ebi.ac.uk <mailto:annelyle at ebi.ac.uk>
> > Web: www.ensembl.org <http://www.ensembl.org/>
> >
> >
> >
> >
> >
> >> On 28 Sep 2015, at 07:37, Dadu <khalandardvg at gmail.com <mailto:
> khalandardvg at gmail.com>> wrote:
> >>
> >> Dear All,
> >>
> >> 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.
> >>
> >> link:
> >> http://asia.ensembl.org/info/docs/webcode/mirror/install/index.html
> >> <http://asia.ensembl.org/info/docs/webcode/mirror/install/index.html>
> >>
> >>
> >> Thanks and regards,
> >> Dadakhalandar
> >> _______________________________________________
> >> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org>
> >> Posting guidelines and subscribe/unsubscribe info:
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> >
> >
> > _______________________________________________
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> >
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> ------------------------------
>
> Message: 2
> Date: Tue, 29 Sep 2015 22:53:19 +0200
> From: Nicolas Thierry-Mieg <Nicolas.Thierry-Mieg at imag.fr>
> Subject: Re: [ensembl-dev] Problem attempting to install VEP 77
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID: <560AFA3F.1080901 at imag.fr>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
>
> 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 .
>
> HTH
>
>
> On 09/29/2015 05:23 PM, Murphy, David wrote:
> > Hi All
> >
> > We?ve been trying to install VEP 77
> > (https://github.com/Ensembl/ensembl-tools/archive/release/77.zip) in
> > order to replicate results from a previous analysis.
> >
> >
> > We?re running perl v5.10.1 on Red Hat Enterprise Linux Server release
> > 6.6 (Santiago)
> >
> > sh-4.1# perl -version
> >
> > This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi
> >
> >
> > When we run Install.pl we get the error
> >
> >
> > sh-4.1# perl INSTALL.pl
> >
> <snip>
> > - unpacking ./Bio/tmp/ensembl.zip
> >
> > Key 'archive' is of invalid type for Archive::Extract::new provided by
> > main::unpack_arch at /usr/share/perl5/Archive/Extract.pm line 270.
> >
> > Can't call method "extract" on an undefined value at INSTALL.pl line 905.
> >
> >
> > The file ensembl.zip  is downloaded and appears to be a valid zip
> > archive and can be extracted manually.
> >
> > The perl core module Archive::Extract appears to be there.
> >
> > Package namespace         installed    latest  in CPAN file
> >
> > Algorithm::Diff              1.1903    1.1903
> > TYEMQ/Algorithm-Diff-1.1903.tar.gz
> >
> > App::cpanminus               1.7039    1.7039
> > MIYAGAWA/App-cpanminus-1.7039.tar.gz
> >
> > Archive::Extract               0.74      0.76
> > BINGOS/Archive-Extract-0.76.tar.gz
> >
> > Archive::Zip                   1.51      1.53
> PHRED/Archive-Zip-1.53.tar.gz
> >
> > Attribute::Handlers            0.85      0.99
> > RJBS/Attribute-Handlers-0.99.tar.gz
> >
> >
> > We also tried with the latest version of the installer to try to
> > diagnose the problem but we got the same error.
> >
> > Any ideas for what might be wrong?
> >
> > Regards
> > David
>
>
>
>
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>
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