[ensembl-dev] Updating dbSNP cosmic and ESP versions
Davineni, Phani Kishore
PDAVINENI at PARTNERS.ORG
Wed Sep 30 21:27:10 BST 2015
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
Send Dev mailing list submissions to
dev at ensembl.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.ensembl.org/mailman/listinfo/dev
or, via email, send a message with subject or body 'help' to
dev-request at ensembl.org
You can reach the person managing the list at
dev-owner at ensembl.org
When replying, please edit your Subject line so it is more specific than "Re: Contents of Dev digest..."
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:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> <http://lists.ensembl.org/mailman/listinfo/dev>
>> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> <http://lists.ensembl.org/mailman/listinfo/dev>
> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.ensembl.org/pipermail/dev/attachments/20150929/de6e370f/attachment.html>
------------------------------
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
------------------------------
_______________________________________________
Dev mailing list Dev at ensembl.org
Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/
End of Dev Digest, Vol 63, Issue 19
***********************************
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
More information about the Dev
mailing list