This code has been forked from the ExAC browser for the purpose of the exomes hosted at UCL (UCLex).
http://phenotips.cs.ucl.ac.uk:8000
The website is currently only accessible if you are on the UCL wired network but you can access it from outside the network by using an ssh tunnel:
ssh -f <username>@jb-gate1.biol.ucl.ac.uk -L1234:phenotips.cs.ucl.ac.uk:8000 -N
Then point your browser to http://localhost:1234.
Create a directory to put all this stuff in. This will serve as the parent directory of the actual uclex_browser repository
mkdir uclex
cd uclex
First (as this can run in parallel), get the datasets that the browser uses and put them into an 'uclex_data' directory:
Now clone the repo:
git clone https://github.com/pontikos/uclex_browser.git
Follow these instructions to get Python and Homebrew installed on your Mac: http://docs.python-guide.org/en/latest/starting/install/osx/
Install MongoDB:
brew install mongodb
# or
sudo port install mongodb
Create a directory to hold your mongo database files:
mkdir database
In a separate tab, start the mongo database server:
mongod --dbpath database
This local server needs to be running at all times when you are working on the site. You could do this in the background if you want or set up some startup service, but I think it's easier just to open a tab you can monitor.
Finally, you may want to keep the system in a virtualenv:
sudo port install py27-virtualenv # Or whatever version
If so, you can create a python virtual environment where the browser will live:
mkdir uclex_env
virtualenv uclex_env
source uclex_env/bin/activate
Install the python requirements:
pip install -r requirements.txt
Note that this installs xBrowse too.
At this point, it's probably worth quickly checking out the code structure if you haven't already :)
Now we must load the database from those flat files. This is a single command, but it can take a while (can take advantage of parallel loads by modifying LOAD_DB_PARALLEL_PROCESSES in uclex.py):
python manage.py load_db
You won't have to run this often - most changes won't require rebuilding the database. That said, this is (and will remain) idempotent, so you can run it again at any time if you think something might be wrong - it will reload the database from scratch. You can also reload parts of the database using any of the following commands:
python manage.py load_variants_file
python manage.py load_dbsnp_file
python manage.py load_base_coverage
python manage.py load_gene_models
Then, you need to create a cache for autocomplete and large gene purposes:
python manage.py create_cache
Note that if you are revisiting the site after a break, make sure your virtualenv is activate'd.
You can run the development server with:
python uclex.py
And visit on your browser:
http://localhost:5000
http://localhost:5000/gene/ENSG00000237683
http://localhost:5000/variant/20-76735-A-T
For testing, you can open up an interactive shell with:
python manage.py shell