[ensembl-dev] Dev Digest, Vol 84, Issue 18

Fri Jun 16 15:25:44 BST 2017

Hi Magali,

Thank you very much ill try it. Can you please point me to instractions
regarding installing your grch37 database? I.E. schema and initial data?

Regards,
Nadav

Once you have installed a local copy of the REST server, you can control
> what data is used via the ensembl_rest.conf file
> https://github.com/Ensembl/ensembl-rest/blob/release/89/
> ensembl_rest.conf.default
> As you can see in the example, it is connecting to our public MySQL
> database, ensembldb.ensembl.org on port 3306.
> To access GRCh37 data, you can simply replace the port with 3337.
> If you are planning on using your local server intensively, we recommend
> you also take a local copy of the databases required.
>
> Hope that helps,
> Magali

On Fri, Jun 16, 2017 at 5:13 PM, <dev-request at ensembl.org> wrote:

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> Today's Topics:
>
>    1. REST-Installation-and-Development for GRCh37 - how to     ?
>       (Nadav Sharabi)
>    2. Re: REST - map endpoint (mag)
>    3. Re: REST-Installation-and-Development for GRCh37 - how to ? (mag)
>    4. Re: REST - map endpoint (Daniel Suveges)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 16 Jun 2017 16:51:21 +0300
> From: Nadav Sharabi <nadav.sharabi at gmail.com>
> To: dev at ensembl.org
> Subject: [ensembl-dev] REST-Installation-and-Development for GRCh37 -
>         how to  ?
> Message-ID:
>         <CAMc0GAk-qtk1-EMR3u7vxNFWCqM7B7zdGBY8JwK6paS
> 4brB2TA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi All,
>
> Can someone please help me understand how to install the vep rest server :
>
> https://github.com/Ensembl/ensembl-rest/wiki/REST-
> Installation-and-Development
>
> but for GRCh37 and not GRCh38 so that i waill have a local copy of
> http://grch37.rest.ensembl.org/ ?
>
> P.S. if i can get access to a ready vagrant or vm that will be really
> helpful.
>
> Best Regards,
> Nadav
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> ------------------------------
>
> Message: 2
> Date: Fri, 16 Jun 2017 14:56:59 +0100
> From: mag <mr6 at ebi.ac.uk>
> To: dev at ensembl.org
> Subject: Re: [ensembl-dev] REST - map endpoint
> Message-ID: <684110b7-8f28-0bba-e6e2-58c826a607b8 at ebi.ac.uk>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Dear Daniel,
>
> Thank you for reporting this, it is definitely not expected behaviour.
> We will investigate the problem and let you know when a fix is available.
>
>
> Kind regards,
> Magali
>
> On 16/06/2017 13:50, Daniel Suveges wrote:
> >
> > Ok, I have to adjust my question: apparently sometimes the query
> > returns the expected coordinates, but mostly the return is empty. I
> > hope this helps.
> >
> > (On the attached screenshot you can see that the response to the same
> > query sometimes empty, sometimes not.)
> >
> > Best,
> >
> > Daniel
> >
> > *From: *Dev <dev-bounces at ensembl.org> on behalf of Daniel Suveges
> > <ds26 at sanger.ac.uk>
> > *Reply-To: *Ensembl developers list <dev at ensembl.org>
> > *Date: *Friday, 16 June 2017 at 13:16
> > *To: *Ensembl developers list <dev at ensembl.org>
> > *Subject: *[ensembl-dev] REST - map endpoint
> >
> > Hi Guys,
> >
> > I?m trying to use the map endpoint of the REST service (to map between
> > the human GRCh37 and 38 build) and I?m encountering some unexpected
> > behavior:
> >
> > Let?s take the variant rs11553699 for example:
> >
> > it?s GRCh37 coordinates: 12:122216910
> >
> > it?s GRCh38 coordinates: 12:121779004
> >
> > If I want to map it?s GRCh37 coordinates to the newer build it works:
> >
> > http://rest.ensembl.org/map/human/GRCh37/12:122216910..
> 122216910:1/GRCh38?content-type=application/json
> >
> > But when I?m trying to do the same in the opposite direction, the
> > ?mappings? array is empty in the returned json:
> >
> > http://rest.ensembl.org/map/human/GRCh38/12:121779004..
> 121779004:1/GRCh37?content-type=application/json
> >
> > For other GRCh38 coordinates mapping works, this position has
> > coordinates in both build, so it is not clear to me why the second
> > query seemingly fails.
> >
> > Thank you very much for your help!
> >
> > Best,
> >
> > Daniel
> >
> >
> >
> > _______________________________________________
> > 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: 3
> Date: Fri, 16 Jun 2017 14:59:32 +0100
> From: mag <mr6 at ebi.ac.uk>
> To: dev at ensembl.org
> Subject: Re: [ensembl-dev] REST-Installation-and-Development for
>         GRCh37 - how to ?
> Message-ID: <c8844c4c-ac95-550d-5c98-a77b4eceb546 at ebi.ac.uk>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Dear Nadav,
>
> Once you have installed a local copy of the REST server, you can control
> what data is used via the ensembl_rest.conf file
> https://github.com/Ensembl/ensembl-rest/blob/release/89/
> ensembl_rest.conf.default
>
> As you can see in the example, it is connecting to our public MySQL
> database, ensembldb.ensembl.org on port 3306.
> To access GRCh37 data, you can simply replace the port with 3337.
>
> If you are planning on using your local server intensively, we recommend
> you also take a local copy of the databases required.
>
>
> Hope that helps,
> Magali
>
> On 16/06/2017 14:51, Nadav Sharabi wrote:
> > Hi All,
> >
> > Can someone please help me understand how to install the vep rest server
> :
> >
> > https://github.com/Ensembl/ensembl-rest/wiki/REST-
> Installation-and-Development
> >
> > but for GRCh37 and not GRCh38 so that i waill have a local copy of
> > http://grch37.rest.ensembl.org/ ?
> >
> > P.S. if i can get access to a ready vagrant or vm that will be really
> > helpful.
> >
> > Best Regards,
> > Nadav
> >
> >
> > _______________________________________________
> > 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: Fri, 16 Jun 2017 13:38:55 +0000
> From: Daniel Suveges <ds26 at sanger.ac.uk>
> To: Ensembl developers list <dev at ensembl.org>
> Subject: Re: [ensembl-dev] REST - map endpoint
> Message-ID: <C312627D-2F34-4DE3-8D6F-A6C32E97C84F at sanger.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Magali,
>
> Thank you very much for your answer! For me it seems that the patch
> (HG1595_PATCH 12:121,761,801-122,096,722) is close but does not overlap
> with this position: 12:122216910. But I might get it wrong, in which case I
> don?t know why this ambiguity is not listed in the variant annotation:
> http://grch37.rest.ensembl.org/variation/human/rs11553699.json
> And does not explain why sometimes I have a proper response. Mysterious.
>
> Best,
> Daniel
>
> From: Dev <dev-bounces at ensembl.org> on behalf of mag <mr6 at ebi.ac.uk>
> Reply-To: Ensembl developers list <dev at ensembl.org>
> Date: Friday, 16 June 2017 at 13:44
> To: "dev at ensembl.org" <dev at ensembl.org>
> Subject: Re: [ensembl-dev] REST - map endpoint
>
> Dear Daniel,
>
> Looking at this region in GRCh37, you can see there is a patch fix
> overlapping.
> http://grch37.ensembl.org/Homo_sapiens/Location/View?r=
> 12:122216910-122216910;db=core
>
> This means that, when attempting to map the region in GRCh38 back to
> GRCh37, there are two possible results, the region on chromosome 12 and the
> region in the patch. As the API will only return unambiguous mappings, the
> query comes back empty.
>
>
> Hope that helps,
> Magali
> On 16/06/2017 13:16, Daniel Suveges wrote:
> Hi Guys,
>
>
> I?m trying to use the map endpoint of the REST service (to map between the
> human GRCh37 and 38 build) and I?m encountering some unexpected behavior:
>
> Let?s take the variant rs11553699 for example:
> it?s GRCh37 coordinates: 12:122216910
> it?s GRCh38 coordinates: 12:121779004
>
> If I want to map it?s GRCh37 coordinates to the newer build it works:
> http://rest.ensembl.org/map/human/GRCh37/12:122216910..
> 122216910:1/GRCh38?content-type=application/json
>
> But when I?m trying to do the same in the opposite direction, the
> ?mappings? array is empty in the returned json:
> http://rest.ensembl.org/map/human/GRCh38/12:121779004..
> 121779004:1/GRCh37?content-type=application/json
>
> For other GRCh38 coordinates mapping works, this position has coordinates
> in both build, so it is not clear to me why the second query seemingly
> fails.
> Thank you very much for your help!
>
> Best,
> Daniel
>
>
>
>
> _______________________________________________
>
> Dev mailing list    Dev at ensembl.org<mailto:Dev at ensembl.org>
>
> Posting guidelines and subscribe/unsubscribe info:
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>
> Ensembl Blog: http://www.ensembl.info/
>
>
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> End of Dev Digest, Vol 84, Issue 18
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