<div dir="ltr"><span style="font-size:12.8px">Hi Magali,</span><div><br></div><div>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?<br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">Regards,</span></div><div>Nadav<br style="font-size:12.8px"><br style="font-size:12.8px"></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span style="font-size:12.8px">Once you have installed a local copy of the REST server, you can control<br></span><span style="font-size:12.8px">what data is used via the ensembl_rest.conf file<br></span><a href="https://github.com/Ensembl/ensembl-rest/blob/release/89/ensembl_rest.conf.default" rel="noreferrer" target="_blank" style="font-size:12.8px">https://github.com/Ensembl/<wbr>ensembl-rest/blob/release/89/<wbr>ensembl_rest.conf.default</a><br style="font-size:12.8px"><span style="font-size:12.8px">As you can see in the example, it is connecting to our public MySQL<br></span><span style="font-size:12.8px">database, </span><a href="http://ensembldb.ensembl.org/" rel="noreferrer" target="_blank" style="font-size:12.8px">ensembldb.ensembl.org</a><span style="font-size:12.8px"> on port 3306.<br></span><span style="font-size:12.8px">To access GRCh37 data, you can simply replace the port with 3337.</span><br style="font-size:12.8px"><span style="font-size:12.8px">If you are planning on using your local server intensively, we recommend<br></span><span style="font-size:12.8px">you also take a local copy of the databases required.</span><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">Hope that helps,<br></span><span style="font-size:12.8px">Magali</span></blockquote></blockquote><div><br style="font-size:12.8px"><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jun 16, 2017 at 5:13 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. REST-Installation-and-<wbr>Development for GRCh37 - how to ?<br>
(Nadav Sharabi)<br>
2. Re: REST - map endpoint (mag)<br>
3. Re: REST-Installation-and-<wbr>Development for GRCh37 - how to ? (mag)<br>
4. Re: REST - map endpoint (Daniel Suveges)<br>
<br>
<br>
------------------------------<wbr>------------------------------<wbr>----------<br>
<br>
Message: 1<br>
Date: Fri, 16 Jun 2017 16:51:21 +0300<br>
From: Nadav Sharabi <<a href="mailto:nadav.sharabi@gmail.com">nadav.sharabi@gmail.com</a>><br>
To: <a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
Subject: [ensembl-dev] REST-Installation-and-<wbr>Development for GRCh37 -<br>
how to ?<br>
Message-ID:<br>
<<a href="mailto:CAMc0GAk-qtk1-EMR3u7vxNFWCqM7B7zdGBY8JwK6paS4brB2TA@mail.gmail.com">CAMc0GAk-qtk1-<wbr>EMR3u7vxNFWCqM7B7zdGBY8JwK6paS<wbr>4brB2TA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi All,<br>
<br>
Can someone please help me understand how to install the vep rest server :<br>
<br>
<a href="https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development" rel="noreferrer" target="_blank">https://github.com/Ensembl/<wbr>ensembl-rest/wiki/REST-<wbr>Installation-and-Development</a><br>
<br>
but for GRCh37 and not GRCh38 so that i waill have a local copy of<br>
<a href="http://grch37.rest.ensembl.org/" rel="noreferrer" target="_blank">http://grch37.rest.ensembl.<wbr>org/</a> ?<br>
<br>
P.S. if i can get access to a ready vagrant or vm that will be really<br>
helpful.<br>
<br>
Best Regards,<br>
Nadav<br>
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Message: 2<br>
Date: Fri, 16 Jun 2017 14:56:59 +0100<br>
From: mag <<a href="mailto:mr6@ebi.ac.uk">mr6@ebi.ac.uk</a>><br>
To: <a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
Subject: Re: [ensembl-dev] REST - map endpoint<br>
Message-ID: <<a href="mailto:684110b7-8f28-0bba-e6e2-58c826a607b8@ebi.ac.uk">684110b7-8f28-0bba-e6e2-<wbr>58c826a607b8@ebi.ac.uk</a>><br>
Content-Type: text/plain; charset="utf-8"; Format="flowed"<br>
<br>
Dear Daniel,<br>
<br>
Thank you for reporting this, it is definitely not expected behaviour.<br>
We will investigate the problem and let you know when a fix is available.<br>
<br>
<br>
Kind regards,<br>
Magali<br>
<br>
On 16/06/2017 13:50, Daniel Suveges wrote:<br>
><br>
> Ok, I have to adjust my question: apparently sometimes the query<br>
> returns the expected coordinates, but mostly the return is empty. I<br>
> hope this helps.<br>
><br>
> (On the attached screenshot you can see that the response to the same<br>
> query sometimes empty, sometimes not.)<br>
><br>
> Best,<br>
><br>
> Daniel<br>
><br>
> *From: *Dev <<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>> on behalf of Daniel Suveges<br>
> <<a href="mailto:ds26@sanger.ac.uk">ds26@sanger.ac.uk</a>><br>
> *Reply-To: *Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
> *Date: *Friday, 16 June 2017 at 13:16<br>
> *To: *Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
> *Subject: *[ensembl-dev] REST - map endpoint<br>
><br>
> Hi Guys,<br>
><br>
> I?m trying to use the map endpoint of the REST service (to map between<br>
> the human GRCh37 and 38 build) and I?m encountering some unexpected<br>
> behavior:<br>
><br>
> Let?s take the variant rs11553699 for example:<br>
><br>
> it?s GRCh37 coordinates: 12:122216910<br>
><br>
> it?s GRCh38 coordinates: 12:121779004<br>
><br>
> If I want to map it?s GRCh37 coordinates to the newer build it works:<br>
><br>
> <a href="http://rest.ensembl.org/map/human/GRCh37/12:122216910..122216910:1/GRCh38?content-type=application/json" rel="noreferrer" target="_blank">http://rest.ensembl.org/map/<wbr>human/GRCh37/12:122216910..<wbr>122216910:1/GRCh38?content-<wbr>type=application/json</a><br>
><br>
> But when I?m trying to do the same in the opposite direction, the<br>
> ?mappings? array is empty in the returned json:<br>
><br>
> <a href="http://rest.ensembl.org/map/human/GRCh38/12:121779004..121779004:1/GRCh37?content-type=application/json" rel="noreferrer" target="_blank">http://rest.ensembl.org/map/<wbr>human/GRCh38/12:121779004..<wbr>121779004:1/GRCh37?content-<wbr>type=application/json</a><br>
><br>
> For other GRCh38 coordinates mapping works, this position has<br>
> coordinates in both build, so it is not clear to me why the second<br>
> query seemingly fails.<br>
><br>
> Thank you very much for your help!<br>
><br>
> Best,<br>
><br>
> Daniel<br>
><br>
><br>
><br>
> ______________________________<wbr>_________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/<wbr>mailman/listinfo/dev</a><br>
> Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br>
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<br>
Message: 3<br>
Date: Fri, 16 Jun 2017 14:59:32 +0100<br>
From: mag <<a href="mailto:mr6@ebi.ac.uk">mr6@ebi.ac.uk</a>><br>
To: <a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
Subject: Re: [ensembl-dev] REST-Installation-and-<wbr>Development for<br>
GRCh37 - how to ?<br>
Message-ID: <<a href="mailto:c8844c4c-ac95-550d-5c98-a77b4eceb546@ebi.ac.uk">c8844c4c-ac95-550d-5c98-<wbr>a77b4eceb546@ebi.ac.uk</a>><br>
Content-Type: text/plain; charset="utf-8"; Format="flowed"<br>
<br>
Dear Nadav,<br>
<br>
Once you have installed a local copy of the REST server, you can control<br>
what data is used via the ensembl_rest.conf file<br>
<a href="https://github.com/Ensembl/ensembl-rest/blob/release/89/ensembl_rest.conf.default" rel="noreferrer" target="_blank">https://github.com/Ensembl/<wbr>ensembl-rest/blob/release/89/<wbr>ensembl_rest.conf.default</a><br>
<br>
As you can see in the example, it is connecting to our public MySQL<br>
database, <a href="http://ensembldb.ensembl.org" rel="noreferrer" target="_blank">ensembldb.ensembl.org</a> on port 3306.<br>
To access GRCh37 data, you can simply replace the port with 3337.<br>
<br>
If you are planning on using your local server intensively, we recommend<br>
you also take a local copy of the databases required.<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
On 16/06/2017 14:51, Nadav Sharabi wrote:<br>
> Hi All,<br>
><br>
> Can someone please help me understand how to install the vep rest server :<br>
><br>
> <a href="https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development" rel="noreferrer" target="_blank">https://github.com/Ensembl/<wbr>ensembl-rest/wiki/REST-<wbr>Installation-and-Development</a><br>
><br>
> but for GRCh37 and not GRCh38 so that i waill have a local copy of<br>
> <a href="http://grch37.rest.ensembl.org/" rel="noreferrer" target="_blank">http://grch37.rest.ensembl.<wbr>org/</a> ?<br>
><br>
> P.S. if i can get access to a ready vagrant or vm that will be really<br>
> helpful.<br>
><br>
> Best Regards,<br>
> Nadav<br>
><br>
><br>
> ______________________________<wbr>_________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/<wbr>mailman/listinfo/dev</a><br>
> Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br>
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<br>
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<br>
Message: 4<br>
Date: Fri, 16 Jun 2017 13:38:55 +0000<br>
From: Daniel Suveges <<a href="mailto:ds26@sanger.ac.uk">ds26@sanger.ac.uk</a>><br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Subject: Re: [ensembl-dev] REST - map endpoint<br>
Message-ID: <<a href="mailto:C312627D-2F34-4DE3-8D6F-A6C32E97C84F@sanger.ac.uk">C312627D-2F34-4DE3-8D6F-<wbr>A6C32E97C84F@sanger.ac.uk</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Magali,<br>
<br>
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:<br>
<a href="http://grch37.rest.ensembl.org/variation/human/rs11553699.json" rel="noreferrer" target="_blank">http://grch37.rest.ensembl.<wbr>org/variation/human/<wbr>rs11553699.json</a><br>
And does not explain why sometimes I have a proper response. Mysterious.<br>
<br>
Best,<br>
Daniel<br>
<br>
From: Dev <<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>> on behalf of mag <<a href="mailto:mr6@ebi.ac.uk">mr6@ebi.ac.uk</a>><br>
Reply-To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Date: Friday, 16 June 2017 at 13:44<br>
To: "<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>" <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Subject: Re: [ensembl-dev] REST - map endpoint<br>
<br>
Dear Daniel,<br>
<br>
Looking at this region in GRCh37, you can see there is a patch fix overlapping.<br>
<a href="http://grch37.ensembl.org/Homo_sapiens/Location/View?r=12:122216910-122216910;db=core" rel="noreferrer" target="_blank">http://grch37.ensembl.org/<wbr>Homo_sapiens/Location/View?r=<wbr>12:122216910-122216910;db=core</a><br>
<br>
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.<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
On 16/06/2017 13:16, Daniel Suveges wrote:<br>
Hi Guys,<br>
<br>
<br>
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:<br>
<br>
Let?s take the variant rs11553699 for example:<br>
it?s GRCh37 coordinates: 12:122216910<br>
it?s GRCh38 coordinates: 12:121779004<br>
<br>
If I want to map it?s GRCh37 coordinates to the newer build it works:<br>
<a href="http://rest.ensembl.org/map/human/GRCh37/12:122216910..122216910:1/GRCh38?content-type=application/json" rel="noreferrer" target="_blank">http://rest.ensembl.org/map/<wbr>human/GRCh37/12:122216910..<wbr>122216910:1/GRCh38?content-<wbr>type=application/json</a><br>
<br>
But when I?m trying to do the same in the opposite direction, the ?mappings? array is empty in the returned json:<br>
<a href="http://rest.ensembl.org/map/human/GRCh38/12:121779004..121779004:1/GRCh37?content-type=application/json" rel="noreferrer" target="_blank">http://rest.ensembl.org/map/<wbr>human/GRCh38/12:121779004..<wbr>121779004:1/GRCh37?content-<wbr>type=application/json</a><br>
<br>
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.<br>
Thank you very much for your help!<br>
<br>
Best,<br>
Daniel<br>
<br>
<br>
<br>
<br>
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End of Dev Digest, Vol 84, Issue 18<br>
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</blockquote></div><br></div>