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CIViC - Clinical Interpretation of Variants in Cancer

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Setup

Prerequisites

Before attempting to install the CIViC server and client software, you should obtain the following applications and libraries:

  • A relatively modern Ruby (>= 1.9.3)
    • If your OS doesn't ship with a modern Ruby, you can use rbenv and ruby-build to obtain it.
  • Postgres
  • NodeJS
  • npm
  • libxml2
  • libxslt
  • libpq-dev
  • openssl

On OSX with homebrew, this should install the needed library dependencies:

brew install libxml2 libxslt openssl postgres node

Installation

The following will set up the server side application and load the database schema.

git clone https://github.com/genome/civic-server.git
cd civic-server
gem install bundler
rbenv rehash
bundle install
rbenv rehash
rake db:create
rake db:structure:load

If re-freshing the database (from a previous install) use rake db:drop before create and structure:load commands. To obtain the initial CIViC data set and load it use:

rake civic:import['import/GeneSummaries.txt','import/VariantSummaries.txt','import/ClinActionEvidence.txt','import/VariantGroupSummaries.txt']

Or alternatively you can load the data from an SQL dump as follows:

rake civic:load

Finally, start the CIViC rails server

rails s

Next, you'll need to set up the client side application using the following:

git clone https://github.com/genome/civic-client.git
cd civic-client
npm install -g bower gulp
npm install
bower install
gulp serve

You should now be able to access the backend server at http://127.0.0.1:3000 and the frontend application at http://127.0.0.1:3001

Note that certain tasks needed by a running instance of CIViC are accomplished by 'background workers'. These can be started on a local instance.For example, we take input a user gives us, and then process it the background (matching up DOIDs, Entrez IDs, etc. with each site's API and adding new items from these sources as needed). If you want to start a backgroun worker locally, you can run (in the civic-server repo):

bin/delayed_job start

Note that the delayed worker job can get into a half baked state that may be cleared by executing this in the rails console: Delayed::Job.all.each { |j| j.delete }

Note to make yourself an admin in a local install you can do the following from your civic-server repo. First log into the front end http://127.0.0.1:3001 and sign in with your user. Log into a rails console, run a command that makes you an admin in the db, and exit.

rails c
User.first.make_admin!
exit

Now log into the backend admin interface as follows: http://127.0.0.1:3000/admin

Note that the above command just makes the first user in the DB an admin. If you have multiple users you could also do:

User.second.make_admin!
User.third.make_admin!

You can run the backend test suite with

rake spec