[ensembl-dev] Dev Digest, Vol 58, Issue 13
Will McLaren
wm2 at ebi.ac.uk
Thu Apr 30 10:35:33 BST 2015
Hello,
Apologies for the delay in replying to this.
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
http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#windows)
If you are not using Windows, did you add any additional parameters when
you ran INSTALL.pl?
Regards
Will McLaren
Ensembl Variation
On 15 April 2015 at 11:31, Santosh Kumar Dodda <
santoshkumar.dodda at bioseed.com> wrote:
> Dear Ensemble team:
>
> 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.
>
> Screen shot:
>
> [image: Inline image 1]
>
> Regards
>
> Santosh Kumar Dodda
> India
>
>
>
> On Tue, Apr 14, 2015 at 4:30 PM, <dev-request at ensembl.org> wrote:
>
>> Send Dev mailing list submissions to
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>>
>> Today's Topics:
>>
>> 1. Re: chain files to build cross-species coordinates conversion
>> (liftover) (Matthieu Muffato)
>> 2. Question about Gene Symbol in cache refseq version (namchul ghim)
>> 3. Re: Question about Gene Symbol in cache refseq version
>> (Will McLaren)
>> 4. Re: Diferen?as entre vers?es (mag)
>> 5. Ensembl Genomes Release 27 Intentions (Dan Staines)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 13 Apr 2015 17:53:47 +0100
>> From: Matthieu Muffato <muffato at ebi.ac.uk>
>> Subject: Re: [ensembl-dev] chain files to build cross-species
>> coordinates conversion (liftover)
>> To: Ensembl developers list <dev at ensembl.org>
>> Message-ID: <552BF49B.5000602 at ebi.ac.uk>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>> Dear Juan-Pascal
>>
>> Even though we do process chains as part of our pairwise-alignment
>> pipelines, the files are not kept, and we rather store the alignment in
>> a more condensed format in the database:
>>
>> http://www.ensembl.org/info/docs/api/compara/compara_schema.html#genomic_align
>>
>> There are two options at this stage (both using the Perl / REST API):
>> either dump the alignment blocks into a chain file to run liftover, or
>> only use the API. They both need to write a piece of code.
>>
>> If you can use the Perl API, there is an example script in the
>> ensembl-compara repository that you'll find useful:
>>
>> https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_convertBasePositionsUsingBlastzAlignments.pl
>> It takes a list of human coordinates and projects them to the chimpanzee
>> genome using our alignment (just change the names of the species).
>>
>> If you are interested in the coordinates of each alignment block, this
>> other script can help:
>>
>> https://github.com/Ensembl/ensembl-compara/blob/release/79/scripts/examples/dna_accessGenomicAlignBlocks.pl
>>
>> Matthieu
>>
>> On 13/04/15 17:18, Juan Pascual Anaya wrote:
>> > Hi Anne,
>> >
>> > Thank you very much for your reply!
>> >
>> > According to those links that I sent about the pairwise alignments I'm
>> > interested in, you can read the following:
>> >
>> > "After running LastZ, the raw LastZ alignment blocks are chained
>> > according to their location in both genomes. During the final netting
>> > process, the best sub-chain is chosen in each region on the reference
>> > species."
>> >
>> > So, I thought that those chain files were already done and available
>> > somewhere.
>> >
>> > I'm using all my genome coordinates from Ensembl (e74), so I guess I
>> > could also use your Assembly Converter tool, but I would still need the
>> > chain files, right? Here:
>> >
>> >
>> http://www.ensembl.org/info/docs/webcode/mirror/tools/assembly_converter.html
>> >
>> > when I try to go to the FTP site where the "current chain files" are,
>> > the site doesn's exist, so I thought that this method is out of date.
>> >
>> > If the Compara team has more info about this, that would be great!
>> >
>> > Thanks!
>> > Juan
>> >
>> >
>> >
>> > On Mon, Apr 13, 2015 at 8:00 PM, <dev-request at ensembl.org
>> > <mailto:dev-request at ensembl.org>> wrote:
>> >
>> >
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>> >
>> > ------------------------------
>> >
>> > Message: 2
>> > Date: Mon, 13 Apr 2015 09:24:21 +0100
>> > From: Anne Lyle <annelyle at ebi.ac.uk <mailto:annelyle at ebi.ac.uk>>
>> > Subject: Re: [ensembl-dev] chain files to build cross-species
>> > coordinates conversion (liftover)
>> > To: Ensembl dev list <dev at ensembl.org <mailto:dev at ensembl.org>>
>> > Message-ID: <326CB180-BB1F-4218-90E6-722656215245 at ebi.ac.uk
>> > <mailto:326CB180-BB1F-4218-90E6-722656215245 at ebi.ac.uk>>
>> > Content-Type: text/plain; charset="utf-8"
>> >
>> > Hi Juan
>> >
>> > We currently only produce chain files (for our own Assembly
>> > Converter) for those species where we?ve done an assembly mapping
>> > through our core pipeline. Perhaps our compara team can chime in
>> > with whether it?s feasible to create them based on pairwise
>> alignments.
>> >
>> > Cheers
>> >
>> > Anne
>> >
>> >
>> > > On 12 Apr 2015, at 09:42, Juan Pascual Anaya <
>> jpascualanaya at gmail.com <mailto:jpascualanaya at gmail.com>> wrote:
>> > >
>> > > Hi Ensembl team,
>> > >
>> > > 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:
>> > >
>> > > Mouse-Chicken pairwise alignment
>> > >http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633
>> > <http://www.ensembl.org/info/genome/compara/mlss.html?mlss=633>
>> > >
>> > > Chicken-Turtle pairwise alignment
>> > >http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657
>> > <http://www.ensembl.org/info/genome/compara/mlss.html?mlss=657>
>> > >
>> > > 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?
>> > >
>> > > Thank you very much,
>> > > Juan
>> > >
>> > > _______________________________________________
>> > > Dev mailing listDev at ensembl.org <mailto:Dev at ensembl.org>
>> > > Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> > > Ensembl Blog:http://www.ensembl.info/
>> >
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>> >
>> > ------------------------------
>> >
>> > _______________________________________________
>> > 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
>> > Ensembl Blog: http://www.ensembl.info/
>> >
>> > --
>> >
>> > Juan Pascual-Anaya, PhD
>> > Research Scientist
>> > Evolutionary Morphology Laboratory, RIKEN
>> > 2-2-3 Minatojima-minamimachi
>> > Chuo-ku, Kobe, Hyogo 650-0047
>> > Japan
>> >
>> >
>> > _______________________________________________
>> > 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/
>> >
>>
>> --
>> Matthieu Muffato, Ph.D.
>> Ensembl Compara and TreeFam Project Leader
>> European Bioinformatics Institute (EMBL-EBI)
>> European Molecular Biology Laboratory
>> Wellcome Trust Genome Campus, Hinxton
>> Cambridge, CB10 1SD, United Kingdom
>> Room A3-145
>> Phone + 44 (0) 1223 49 4631
>> Fax + 44 (0) 1223 49 4468
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 14 Apr 2015 08:30:03 +0900
>> From: namchul ghim <chulghim at gmail.com>
>> Subject: [ensembl-dev] Question about Gene Symbol in cache refseq
>> version
>> To: Ensembl developers list <Dev at ensembl.org>
>> Message-ID:
>> <CANi7z4f4ES1unbNnQ34ErHhVF9VDWm99MqsK2z=
>> XD5UU4id4aw at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> In Refseq version, SYMBOL field is blank.
>>
>> How can i get SYMBOL value in cache refseq version ?
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>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 14 Apr 2015 08:48:04 +0100
>> From: Will McLaren <wm2 at ebi.ac.uk>
>> Subject: Re: [ensembl-dev] Question about Gene Symbol in cache refseq
>> version
>> To: Ensembl developers list <dev at ensembl.org>
>> Message-ID:
>> <
>> CAMVEDX1s0CzWzjLY00qY23qxAGrrh6mULhDj8gBE2685WiGLoQ at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Namchul,
>>
>> This was fixed already (in reply to your question in fact!).
>>
>> Please make sure your API is up to date; if you still experience an issue
>> with this, can you please provide a sample of input and the command line
>> that you are using that recreates the problem?
>>
>> Thanks
>>
>> Will
>>
>> On 14 April 2015 at 00:30, namchul ghim <chulghim at gmail.com> wrote:
>>
>> > In Refseq version, SYMBOL field is blank.
>> >
>> > How can i get SYMBOL value in cache refseq version ?
>> >
>> >
>> > _______________________________________________
>> > 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/
>> >
>> >
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>>
>> ------------------------------
>>
>> Message: 4
>> Date: Tue, 14 Apr 2015 09:05:50 +0100
>> From: mag <mr6 at ebi.ac.uk>
>> Subject: Re: [ensembl-dev] Diferen?as entre vers?es
>> To: Ensembl developers list <dev at ensembl.org>
>> Message-ID: <552CCA5E.6060903 at ebi.ac.uk>
>> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>>
>> Hi Igo,
>>
>> The versions represent the releases.
>> Each release, we update the databases and provide a new webserver,
>> retiring the older version.
>> Updates can include new data, updated data, updated schemas or new
>> display features.
>>
>> You can check what has changed for a given release on the news page:
>> http://www.ensembl.org/info/website/news_by_topic.html
>>
>>
>> Hope that helps,
>> Magali
>>
>> On 13/04/2015 15:21, Igo Medeiros wrote:
>> > What are the main differences between the databases's versions in
>> > ensembl? How can i find in the documentation?
>> >
>> > --
>> > Igo Paix?o de Medeiros
>> >
>> >
>> > _______________________________________________
>> > 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/
>>
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>>
>> ------------------------------
>>
>> Message: 5
>> Date: Tue, 14 Apr 2015 09:12:08 +0100
>> From: Dan Staines <dstaines at ebi.ac.uk>
>> Subject: [ensembl-dev] Ensembl Genomes Release 27 Intentions
>> To: dev at ensembl.org
>> Message-ID: <552CCBD8.5010708 at ebi.ac.uk>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>> Dear all,
>>
>> Release 27 of Ensembl Genomes is scheduled for 26th May 2015 - our
>> intentions for this release can be found here:
>> http://ensemblgenomes.org/info/release/27
>> Please note these are intentions and are therefore not guaranteed to be
>> completed for May.
>>
>> Best regards,
>>
>> Dan Staines, on behalf of the Ensembl Genomes team.
>>
>> --
>> Dan Staines, PhD Ensembl Genomes Technical Coordinator
>> EMBL-EBI Tel: +44-(0)1223-492507
>> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> 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 58, Issue 13
>> ***********************************
>>
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