[ensembl-dev] VM with rest API
Andy Yates
ayates at ebi.ac.uk
Tue Aug 20 17:16:48 BST 2013
Hi Brett,
You'll need the human variation database IIRC. REST VEP is not compatible with the caches yet
Andy
------------
Andrew Yates - Ensembl Core Software Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
http://www.ensembl.org/
On 20 Aug 2013, at 17:08, Brett Thomas <bthomas at atgu.mgh.harvard.edu> wrote:
> Hey Andy + Emily --
>
> First, *thank you* for this fantastic writeup. It worked perfectly and helped isolate the issue. Problem is with my ensembl database, not the rest code.
>
> When I use the VEP rest interface with useastdb.ensembl.org, it works. When I use my local database, I get the same error [1]. All the endpoints other than VEP work, for example /feature/id.
>
> Does VEP require additional databases? Here's what I have:
>
> mysql> show databases;
> +-------------------------+
> | Database |
> +-------------------------+
> | information_schema |
> | ensembl_accounts |
> | ensembl_ontology_72 |
> | ensembl_website_72 |
> | homo_sapiens_core_72_37 |
> | mysql |
> | performance_schema |
> | test |
> +-------------------------+
> 8 rows in set (0.00 sec)
>
>
> Thanks --
> Brett
>
> [1] Ensembl log:
>
> 2013/08/20 16:02:08 (5200) Catalyst.pm 1988> *** Request 1 (0.167/s) [11059] [Tue Aug 20 16:02:08 2013] ***
> 2013/08/20 16:02:08 (1) Dispatcher.pm 387> Path is "/vep/get_consequences"
> 2013/08/20 16:02:08 (0) Catalyst.pm 2227> "GET" request for "vep/human/1:6524705:6524705/T/consequences" from "10.0.2.2"
> 2013/08/20 16:02:08 (1) Registry.pm 54> Loading the registry model object
> 2013/08/20 16:02:08 (0) Registry.pm 70> Using host settings from the configuration file
> 2013/08/20 16:02:08 (14) Registry.pm 107> Setting up connection policies
> 2013/08/20 16:02:08 (0) Registry.pm 115> Setting all DBAdaptors to reconnect when connections are lost
> 2013/08/20 16:02:08 (0) Registry.pm 120> Stopping caching in all adaptors and clearing out existing caches
> 2013/08/20 16:02:08 (0) Registry.pm 128> Connection sharing turned on
> 2013/08/20 16:02:08 (0) Registry.pm 141> Using reconnect_interval of 600000
> 2013/08/20 16:02:08 (0) Registry.pm 151> New connection being generated for mysql DB at mysqldba at localhost:5306
> 2013/08/20 16:02:08 (1) ReturnError.pm 40> stash takes a hash or hashref at /usr/local/lib/perl/5.14.2/Class/MOP/Method/Wrapped.pm line 162.
> 2013/08/20 16:02:08 (0) REST.pm 485> Status Bad Request: something bad has happened
> 2013/08/20 16:02:08 (10) Serialize.pm 45> Serializing with Catalyst::Action::Serialize::YAML::HTML
> 2013/08/20 16:02:08 (1) Catalyst.pm 2278> Response Code: 400; Content-Type: text/html; Content-Length: 104
> 2013/08/20 16:02:08 (0) Catalyst.pm 1833> Request took 0.033043s (30.264/s)
> .------------------------------------------------------------+-----------.
> | Action | Time |
> +------------------------------------------------------------+-----------+
> | /vep/begin | 0.000121s |
> | /vep/get_species | 0.029161s |
> | /returnerror/begin | 0.000119s |
> | /returnerror/from_ensembl | 0.000585s |
> | -> returnerror/from_ensembl_GET | 0.000050s |
> | /returnerror/end | 0.010666s |
> '------------------------------------------------------------+-----------'
>
>
>
>
>
> On Mon, Aug 19, 2013 at 5:59 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> Hi Brett,
>
> As Emily says we can help you out if you send us your error messages. We do not ship a VM with a working rest api for download. However you should be able to take the normal Ensembl VM (ftp://ftp.ensembl.org/pub/release-72/virtual_machine/Ensembl72VirtualMachine.ova) and supplement it with the rest server. This does take a little bit of mucking around in the VM because of some odd dependency issues in our VM. This is also an Ubuntu server so hopefully some of the steps will be familiar/directly applicable to your situation:
>
> # First we need to add the following repos to the /etc/apt/sources.list (due to missing dependencies)
> deb http://ca.archive.ubuntu.com/ubuntu/ precise-updates main restricted
> deb http://ca.archive.ubuntu.com/ubuntu/ precise-updates universe
> deb http://ca.archive.ubuntu.com/ubuntu/ precise-updates multiverse
>
> # Refresh apt
> sudo apt-get update
>
> # Bring in cpanminus & Module::Install from apt-get; sudo password is "ensembl"
> sudo apt-get install cpanminus libmodule-install-perl
> sudo apt-get install libxml-libxml-perl libtest-xml-simple-perl
>
> # Install Catalyst and its development dependencies
> cpanm --sudo Catalyst Catalyst::Devel
>
> # Now install the REST server
> cd ~/ensembl-api-folder
>
> cvs -d :pserver:cvsuser at cvs.sanger.ac.uk:/cvsroot/ensembl login
> CVS password: CVSUSER
>
> cvs -d :pserver:cvsuser at cvs.sanger.ac.uk:/cvsroot/ensembl co -r branch-ensembl-72 ensembl-rest
>
> cd ensembl-rest
>
> #Bring in the dependencies for REST; this will take a long time to finish
> cpanm --sudo --installdeps .
>
> $EDITOR ensembl_rest.conf
> #Edit the connection settings accordingly
>
> perl scripts/ensembl_rest_server.pl
>
> This should start up a server on your VM on port 3000. To test the server go to
>
> http://localhost:3000/vep/human/9:22125503-22125502:1/C/consequences?content-type=application/json
>
> All the best,
>
> Andy
>
> ------------
> Andrew Yates - Ensembl Core Software Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> Tel: +44-(0)1223-492538
> Fax: +44-(0)1223-494468
> http://www.ensembl.org/
>
> On 18 Aug 2013, at 03:08, Brett Thomas <bthomas at atgu.mgh.harvard.edu> wrote:
>
> > Hey dev -- is there a VM that has the rest API installed out of the box?
> >
> > I'm trying to install on a clean ubuntu VM, and can't get VEP + rest to play nice. All of the other endpoints work great, but the vep ones keep failing with a cryptic Catalyst error: "stash takes a hash or hashref"
> >
> > I've tried a few different library permutations but can't get it working. If anybody has suggestions about the error above I'd love to hear them - but otherwise, I was hoping to inspect a working version to see what's different.
> >
> > Thanks --
> > Brett
> > _______________________________________________
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>
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