The application is targeted at python 3.6. It will most likely work with later versions as well.
venv
is not a requirement but it will help you to install the application.
Download the repository from github
Make sure you have registered an Elixir AAI application with the Elixir.
Rename the file settings_sample.json
into settings.json
and edit all
the values.
If you have venv
and pip
available you can do the following
to install the required Python packages:
python -m venv venv-folder
source /path/to/venv-folder/bin/activate # activate your virtual environment
pip install -r /path/to/requrements.txt # install the required Python packages
backend/requirements.txt
scripts/importer/requirements.txt
docs/requirements.txt
Create the PostgreSQL database and its tables with the following command:
psql -U postgres -h 127.0.0.1 -f sql/data_schema.sql
psql -U postgres -h 127.0.0.1 -f sql/user_schema.sql
To experience the full site you need to manually add a dataset and a user to the database.
You can use the test data in test/data/browser_test_data.sql
as reference.
Add reference data and variants using the import scripts found in scripts/
, e.g.:
./manage.sh import --add_reference \
--gencode_version 19 \
--ensembl_version homo_sapiens_core_75_37 \
--assembly_id GRCh37p13 \
--dbnsfp_version 2.9.3 \
--ref_name GRCh37p13
./manage.sh import --add_raw_data \
--dataset variant_data \
--version 20190415 \
--variant_file variants/chr22.vcf.gz \
--coverage_file coverage/chr22.coverage.txt.gz
source /path/to/bin/activate # activate your virtual environment
python /path/to/route.py
docker-compose up
psql -h localhost -U postgres swefreq -f test/data/browser_test_data.sql