draft for updated readme

README.md

@@ -7,53 +7,61 @@ SweFreq - Swedish Frequency database
 Running on a production system
 ------------------------------
 
-The application has only been tested with python 3.5.2. It will most likely work with at least other 3.5 versions.
+The application is targeted at python 3.6. It will most likely work with 3.5 and 3.7 as well.
 
-`virtualenv` is not a requirement but it will help you to install the application.
+`venv` is not a requirement but it will help you to install the application.
 
 1. Download the repository from [github](https://github.com/NBISweden/swefreq)
 
 2. Credentials
 
    2.1 Make sure you have registered an Elixir AAI application with the Elixir.
 
-   2.2 (legacy) Create Google OAuth 2.0 credentials with the [Google API
-   Console](https://console.developers.google.com/) for enabling
-   authentication.
-
 3. Rename the file `settings_sample.json` into `settings.json` and edit all
    the values.
 
-4. Install MySQL. Only tested with 5.6. Note, the schema is incompatible with the
-   latest version of MariaDB.
-
-5. If you have `virtualenv` and `pip` installed then you can do the following
+5. If you have `venv` and `pip` installed then you can do the following
    to install the required Python packages. Locate the `requirements.txt` file
    in the `swefreq` repository.
 
-    source /path/to/bin/activate             # activate your virtualenv
-    pip install -r /path/to/requrements.txt  # install the required Python packages
+   ```
+   source /path/to/bin/activate             # activate your virtual environment
+   pip install -r /path/to/requrements.txt  # install the required Python packages
+   ````
+
+6. Create the PostgreSQL database and its tables with the following command:
 
-6. Create the MySQL database, user and 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
+   ```
 
-       mysql -u root -p < ./sql/swefreq.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`.
 
-   To experience the full site you need to manually add a dataset and a user
-   to the database. Log into the mysql console and enter something like the
-   following, change the values to whatever fits your site (N.B.
-   `myemail@google.com` is your google id):
+7. Add reference data and variants using the import scripts found in `scripts/`, e.g.:
 
-       USE swefreq;
-       INSERT INTO dataset (dataset_pk, name) VALUES (1, "Dataset");
-       INSERT INTO user (user_pk,name, email) VALUES (1, "test", "myemail@google.com");
-       INSERT INTO dataset_access (dataset_pk, user_pk, is_admin, has_access) VALUES (1,1,1,1);
+   ```
+   ./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 virtualenv
+```
+    source /path/to/bin/activate                   # activate your virtual environment
     python /path/to/route.py
-
+```
 
 Quick development mode
 ----------------------