Before attempting to install the CIViC client and server 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
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:schema:load
If re-freshing the database (from a previous install) use rake db:drop before create and schema: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 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!, etc.