[ensembl-dev] VM with rest API

Andy Yates ayates at ebi.ac.uk
Mon Aug 19 10:59:06 BST 2013


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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