<div dir="ltr">Hello,<div><br></div><div>Apologies for the delay in replying to this.</div><div><br></div><div>What are the details of your system? It looks to me like perhaps you are running under Windows; if so, I'd suggest you try installing VEP under cygwin instead of trying to use ActiveState Perl natively (see <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#windows">http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#windows</a>)</div><div><br></div><div>If you are not using Windows, did you add any additional parameters when you ran INSTALL.pl?</div><div><br></div><div>Regards</div><div><br>Will McLaren</div><div>Ensembl Variation</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 15 April 2015 at 11:31, Santosh Kumar Dodda <span dir="ltr"><<a href="mailto:santoshkumar.dodda@bioseed.com" target="_blank">santoshkumar.dodda@bioseed.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 class="gmail_default" style="font-family:verdana,sans-serif;color:rgb(0,0,0)">Dear Ensemble team:</div><div class="gmail_default" style="font-family:verdana,sans-serif;color:rgb(0,0,0)"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;color:rgb(0,0,0)">I am trying to install the refseq using the perl script for VEP. I have tried doing it for two species viz homo_sapiens and Solanum Lycopersicum, unfortunately both the installations got failed. For you reference I am attaching a screen shot. Please help me in this regard.</div><div class="gmail_default" style="font-family:verdana,sans-serif;color:rgb(0,0,0)"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;color:rgb(0,0,0)">Screen shot:</div><div class="gmail_default" style="font-family:verdana,sans-serif;color:rgb(0,0,0)"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;color:rgb(0,0,0)"><img src="cid:ii_14cbca0ae1be5d55" alt="Inline image 1" width="394" height="328"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;color:rgb(0,0,0)"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;color:rgb(0,0,0)">Regards</div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><font face="comic sans ms, sans-serif" color="#0000ff">Santosh Kumar Dodda</font><br></div><div><div class="gmail_default" style="font-family:verdana,sans-serif;color:rgb(0,0,0)">India</div><br></div><div><br></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Apr 14, 2015 at 4:30 PM, <span dir="ltr"><<a href="mailto:dev-request@ensembl.org" target="_blank">dev-request@ensembl.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Dev mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: chain files to build cross-species coordinates conversion<br>
(liftover) (Matthieu Muffato)<br>
2. Question about Gene Symbol in cache refseq version (namchul ghim)<br>
3. Re: Question about Gene Symbol in cache refseq version<br>
(Will McLaren)<br>
4. Re: Diferen?as entre vers?es (mag)<br>
5. Ensembl Genomes Release 27 Intentions (Dan Staines)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 13 Apr 2015 17:53:47 +0100<br>
From: Matthieu Muffato <<a href="mailto:muffato@ebi.ac.uk" target="_blank">muffato@ebi.ac.uk</a>><br>
Subject: Re: [ensembl-dev] chain files to build cross-species<br>
coordinates conversion (liftover)<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
Message-ID: <<a href="mailto:552BF49B.5000602@ebi.ac.uk" target="_blank">552BF49B.5000602@ebi.ac.uk</a>><br>
Content-Type: text/plain; charset=windows-1252; format=flowed<br>
<br>
Dear Juan-Pascal<br>
<br>
Even though we do process chains as part of our pairwise-alignment<br>
pipelines, the files are not kept, and we rather store the alignment in<br>
a more condensed format in the database:<br>
<a href="http://www.ensembl.org/info/docs/api/compara/compara_schema.html#genomic_align" target="_blank">http://www.ensembl.org/info/docs/api/compara/compara_schema.html#genomic_align</a><br>
<br>
There are two options at this stage (both using the Perl / REST API):<br>
either dump the alignment blocks into a chain file to run liftover, or<br>
only use the API. They both need to write a piece of code.<br>
<br>
If you can use the Perl API, there is an example script in the<br>
ensembl-compara repository that you'll find useful:<br>
<a href="https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_convertBasePositionsUsingBlastzAlignments.pl" target="_blank">https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_convertBasePositionsUsingBlastzAlignments.pl</a><br>
It takes a list of human coordinates and projects them to the chimpanzee<br>
genome using our alignment (just change the names of the species).<br>
<br>
If you are interested in the coordinates of each alignment block, this<br>
other script can help:<br>
<a href="https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_accessGenomicAlignBlocks.pl" target="_blank">https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_accessGenomicAlignBlocks.pl</a><br>
<br>
Matthieu<br>
<br>
On 13/04/15 17:18, Juan Pascual Anaya wrote:<br>
> Hi Anne,<br>
><br>
> Thank you very much for your reply!<br>
><br>
> According to those links that I sent about the pairwise alignments I'm<br>
> interested in, you can read the following:<br>
><br>
> "After running LastZ, the raw LastZ alignment blocks are chained<br>
> according to their location in both genomes. During the final netting<br>
> process, the best sub-chain is chosen in each region on the reference<br>
> species."<br>
><br>
> So, I thought that those chain files were already done and available<br>
> somewhere.<br>
><br>
> I'm using all my genome coordinates from Ensembl (e74), so I guess I<br>
> could also use your Assembly Converter tool, but I would still need the<br>
> chain files, right? Here:<br>
><br>
> <a href="http://www.ensembl.org/info/docs/webcode/mirror/tools/assembly_converter.html" target="_blank">http://www.ensembl.org/info/docs/webcode/mirror/tools/assembly_converter.html</a><br>
><br>
> when I try to go to the FTP site where the "current chain files" are,<br>
> the site doesn's exist, so I thought that this method is out of date.<br>
><br>
> If the Compara team has more info about this, that would be great!<br>
><br>
> Thanks!<br>
> Juan<br>
><br>
><br>
><br>
> On Mon, Apr 13, 2015 at 8:00 PM, <<a href="mailto:dev-request@ensembl.org" target="_blank">dev-request@ensembl.org</a><br>
> <mailto:<a href="mailto:dev-request@ensembl.org" target="_blank">dev-request@ensembl.org</a>>> wrote:<br>
><br>
><br>
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><br>
> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Mon, 13 Apr 2015 09:24:21 +0100<br>
> From: Anne Lyle <<a href="mailto:annelyle@ebi.ac.uk" target="_blank">annelyle@ebi.ac.uk</a> <mailto:<a href="mailto:annelyle@ebi.ac.uk" target="_blank">annelyle@ebi.ac.uk</a>>><br>
> Subject: Re: [ensembl-dev] chain files to build cross-species<br>
> coordinates conversion (liftover)<br>
> To: Ensembl dev list <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>>><br>
> Message-ID: <<a href="mailto:326CB180-BB1F-4218-90E6-722656215245@ebi.ac.uk" target="_blank">326CB180-BB1F-4218-90E6-722656215245@ebi.ac.uk</a><br>
> <mailto:<a href="mailto:326CB180-BB1F-4218-90E6-722656215245@ebi.ac.uk" target="_blank">326CB180-BB1F-4218-90E6-722656215245@ebi.ac.uk</a>>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> Hi Juan<br>
><br>
> We currently only produce chain files (for our own Assembly<br>
> Converter) for those species where we?ve done an assembly mapping<br>
> through our core pipeline. Perhaps our compara team can chime in<br>
> with whether it?s feasible to create them based on pairwise alignments.<br>
><br>
> Cheers<br>
><br>
> Anne<br>
><br>
><br>
> > On 12 Apr 2015, at 09:42, Juan Pascual Anaya <<a href="mailto:jpascualanaya@gmail.com" target="_blank">jpascualanaya@gmail.com</a> <mailto:<a href="mailto:jpascualanaya@gmail.com" target="_blank">jpascualanaya@gmail.com</a>>> wrote:<br>
> ><br>
> > Hi Ensembl team,<br>
> ><br>
> > I am currently doing a comparative analysis of some ChIP-seq datasets between mouse, chicken and turtle (P. sinensis). Therefore, I was interested in getting a cross-species coordinate conversion, like assembly converter or liftover. I've seen that you have these two pairwise alignments done:<br>
> ><br>
> > Mouse-Chicken pairwise alignment<br>
> ><a href="http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633" target="_blank">http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633</a><br>
> <<a href="http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633" target="_blank">http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633</a>><br>
> ><br>
> > Chicken-Turtle pairwise alignment<br>
> ><a href="http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657" target="_blank">http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657</a><br>
> <<a href="http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657" target="_blank">http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657</a>><br>
> ><br>
> > So, I was wondering if I could get the best subset of chains from your LASTZ-net results (i.e., the liftover chain files) so that I can do myself a liftOver. I have not seen this files for download in the Ensembl webpage, so could you let me know how to get them?<br>
> ><br>
> > Thank you very much,<br>
> > Juan<br>
> ><br>
> > _______________________________________________<br>
> > Dev mailing <a href="mailto:listDev@ensembl.org" target="_blank">listDev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
> > Posting guidelines and subscribe/unsubscribe info:<a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
> > Ensembl Blog:<a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
><br>
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><br>
> ------------------------------<br>
><br>
> _______________________________________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
> Posting guidelines and subscribe/unsubscribe info:<br>
> <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
> Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
><br>
> --<br>
><br>
> Juan Pascual-Anaya, PhD<br>
> Research Scientist<br>
> Evolutionary Morphology Laboratory, RIKEN<br>
> 2-2-3 Minatojima-minamimachi<br>
> Chuo-ku, Kobe, Hyogo 650-0047<br>
> Japan<br>
><br>
><br>
> _______________________________________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
> Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
><br>
<br>
--<br>
Matthieu Muffato, Ph.D.<br>
Ensembl Compara and TreeFam Project Leader<br>
European Bioinformatics Institute (EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus, Hinxton<br>
Cambridge, CB10 1SD, United Kingdom<br>
Room A3-145<br>
Phone + 44 (0) 1223 49 4631<br>
Fax + 44 (0) 1223 49 4468<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 14 Apr 2015 08:30:03 +0900<br>
From: namchul ghim <<a href="mailto:chulghim@gmail.com" target="_blank">chulghim@gmail.com</a>><br>
Subject: [ensembl-dev] Question about Gene Symbol in cache refseq<br>
version<br>
To: Ensembl developers list <<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
Message-ID:<br>
<CANi7z4f4ES1unbNnQ34ErHhVF9VDWm99MqsK2z=<a href="mailto:XD5UU4id4aw@mail.gmail.com" target="_blank">XD5UU4id4aw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
In Refseq version, SYMBOL field is blank.<br>
<br>
How can i get SYMBOL value in cache refseq version ?<br>
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<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 14 Apr 2015 08:48:04 +0100<br>
From: Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>><br>
Subject: Re: [ensembl-dev] Question about Gene Symbol in cache refseq<br>
version<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAMVEDX1s0CzWzjLY00qY23qxAGrrh6mULhDj8gBE2685WiGLoQ@mail.gmail.com" target="_blank">CAMVEDX1s0CzWzjLY00qY23qxAGrrh6mULhDj8gBE2685WiGLoQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Namchul,<br>
<br>
This was fixed already (in reply to your question in fact!).<br>
<br>
Please make sure your API is up to date; if you still experience an issue<br>
with this, can you please provide a sample of input and the command line<br>
that you are using that recreates the problem?<br>
<br>
Thanks<br>
<br>
Will<br>
<br>
On 14 April 2015 at 00:30, namchul ghim <<a href="mailto:chulghim@gmail.com" target="_blank">chulghim@gmail.com</a>> wrote:<br>
<br>
> In Refseq version, SYMBOL field is blank.<br>
><br>
> How can i get SYMBOL value in cache refseq version ?<br>
><br>
><br>
> _______________________________________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info:<br>
> <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
> Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
><br>
><br>
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<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 14 Apr 2015 09:05:50 +0100<br>
From: mag <<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>><br>
Subject: Re: [ensembl-dev] Diferen?as entre vers?es<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
Message-ID: <<a href="mailto:552CCA5E.6060903@ebi.ac.uk" target="_blank">552CCA5E.6060903@ebi.ac.uk</a>><br>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
<br>
Hi Igo,<br>
<br>
The versions represent the releases.<br>
Each release, we update the databases and provide a new webserver,<br>
retiring the older version.<br>
Updates can include new data, updated data, updated schemas or new<br>
display features.<br>
<br>
You can check what has changed for a given release on the news page:<br>
<a href="http://www.ensembl.org/info/website/news_by_topic.html" target="_blank">http://www.ensembl.org/info/website/news_by_topic.html</a><br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
On 13/04/2015 15:21, Igo Medeiros wrote:<br>
> What are the main differences between the databases's versions in<br>
> ensembl? How can i find in the documentation?<br>
><br>
> --<br>
> Igo Paix?o de Medeiros<br>
><br>
><br>
> _______________________________________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
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<br>
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<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Tue, 14 Apr 2015 09:12:08 +0100<br>
From: Dan Staines <<a href="mailto:dstaines@ebi.ac.uk" target="_blank">dstaines@ebi.ac.uk</a>><br>
Subject: [ensembl-dev] Ensembl Genomes Release 27 Intentions<br>
To: <a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
Message-ID: <<a href="mailto:552CCBD8.5010708@ebi.ac.uk" target="_blank">552CCBD8.5010708@ebi.ac.uk</a>><br>
Content-Type: text/plain; charset=utf-8; format=flowed<br>
<br>
Dear all,<br>
<br>
Release 27 of Ensembl Genomes is scheduled for 26th May 2015 - our<br>
intentions for this release can be found here:<br>
<a href="http://ensemblgenomes.org/info/release/27" target="_blank">http://ensemblgenomes.org/info/release/27</a><br>
Please note these are intentions and are therefore not guaranteed to be<br>
completed for May.<br>
<br>
Best regards,<br>
<br>
Dan Staines, on behalf of the Ensembl Genomes team.<br>
<br>
--<br>
Dan Staines, PhD Ensembl Genomes Technical Coordinator<br>
EMBL-EBI Tel: <a href="tel:%2B44-%280%291223-492507" value="+441223492507" target="_blank">+44-(0)1223-492507</a><br>
Wellcome Trust Genome Campus Fax: <a href="tel:%2B44-%280%291223-494468" value="+441223494468" target="_blank">+44-(0)1223-494468</a><br>
Cambridge CB10 1SD, UK <a href="http://www.ensemblgenomes.org/" target="_blank">http://www.ensemblgenomes.org/</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
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Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
<br>
End of Dev Digest, Vol 58, Issue 13<br>
***********************************<br>
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