SweFreq - Swedish Frequency database

Running on a production system

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.

1. Download the repository from github

2. Make sure you have registered an Elixir AAI application with the Elixir.

3. Rename the file settings_sample.json into settings.json and edit all the values.

4. 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: backend/requirements.txt
   • importer: scripts/importer/requirements.txt
   • documentation: docs/requirements.txt

5. 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.

6. 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
   

Start the server

    source /path/to/bin/activate                   # activate your virtual environment
    python /path/to/route.py

Quick development mode

1. Install docker (and docker-compose in case it's not included in the installation)
2. Run the server:

docker-compose up

3. Add test data to db:

psql -h localhost -U postgres swefreq -f test/data/browser_test_data.sql

Database Schema

---
config:
  layout: elk
  look: handDrawn
  theme: default
---
erDiagram
    GENES |{--|| REFERENCE_SETS : reference_set
    GENE_OTHER_NAMES |{--|| GENES : gene
    TRANSCRIPTS |{--|| GENES : gene
    FEATURES |{--|| GENES : gene
    FEATURES |{--|| TRANSCRIPTS : transcript

    DATASETS |{--|| STUDY : STUDY
    DATASET_LOGOS ||--|| DATASETS : dataset
    SAMPLE_SETS |{--|| DATASETS : dataset
    SAMPLE_SETS |{--|| COLLECTIONS : collection
    DATASET_VERSIONS |{--|| DATASETS : dataset
    DATASET_VERSIONS |{--|| REFERENCE_SETS : reference_set
    DATASET_FILES |{--|| DATASET_VERSIONS : dataset_version

    VARIANTS |{--|| DATASET_VERSIONS : dataset_version
    MATES |{--|| DATASET_VERSIONS : dataset_version
    GENES |{--}| VARIANTS : gene_variant
    COVERAGE |{--|| DATASET_VERSIONS : dataset_version
    METRICS |{--|| DATASET_VERSIONS : dataset_version

Loading