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INSTALLATION.md

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Installation

These instructions will allow you to install the package and accompanying databases on Linux. Mac OS X computers operate similarly. For any other systems, or if you cannot install the databases, we recommend installing via docker.

Pre-requisites

Required:

  • MySQL
  • Python 3.6 or above
  • SQLite version 3.8.0 or above

Optional:

  • PostgreSQL version 10.5 or above.

Download the source code

To download the VariantValidator source code simply clone the master branch.

$ git clone https://github.com/openvar/variantValidator.git
$ cd variantValidator/

Python 3.6 environment

When installing VariantValidator we recommend using a virtual environment, as it requires specific versions of several libraries including python and sqlite. This can be done either via conda or pip.

Via conda

After installing conda you can create a new virtual environment with the correct python and sqlite versions by running:

$ conda env create -f environment.yml
$ conda activate vvenv

The packages required for VariantValidator to function are now set up in the environment "vvenv".

Via pip

If you already have the right versions of python (>=3.6) and sqlite (>=3.8), then you can use pip to BT create a new virtual envionment and install the packages required for VariantValidator to function.

$ python -m venv vvenv
$ source activate vvenv
$ pip install -r requirements.txt

Additional steps for running MariaDB

Install the mariadb python library

Note: Only do this if you intend to run MariaDB instead of MySQL

$ pip install mariadb

Additional steps may be required Install MariaDB Connector/C Installation instructions can be found here

Installing VariantValidator

Hint: your new environment vvenv should still be activated from the previous steps and you should still be in the /variantValidator directory where setup.py is located.

To install VariantValidator within your virtual environment run:

$ pip install -e .

Setting up validator database (MySQL)

A MySQL database called validator is required to run VariantValidator. We recommend creating a user and password specific to the validator database, for example:

CREATE USER 'USER'@'HOST' IDENTIFIED WITH mysql_native_password BY 'PASSWORD';
CREATE DATABASE validator;
GRANT SELECT,INSERT,UPDATE,DELETE ON validator.* TO 'USER'@'HOST';

Where:

  • USER should be a user-name e.g. vvadmin
  • HOST is the MySQL host ID, usually 127.0.0.1
  • PASSWORD is a unique password for your database

Note: We have had reports that on some systems ALL PRIVILEGES may be required rather than SELECT,INSERT,UPDATE,DELETE

Download and our pre-populated database to MySQL as follows.

Essential Step: check here and make sure you download and install the most up-to-date version

$ wget https://www528.lamp.le.ac.uk/vvdata/validator/validator_202x-xx-xx.sql.gz
$ gunzip validator_202x-xx-xx.sql.gz
$ mysql validator < validator_202x-xx-xx.sql -u HOST -p

See the Manual for instructions on updating this database, which should be done regularly.

If you wish to test your installation using pytest (see below) we recommend that you do this before updating the database.

Setting up Seqrepo (SQLite >=3.8)

VariantValidator requires a local SeqRepo database. The seqrepo package has already been installed into the virtual environment, but you'll need to download an actual seqrepo database. This can go anywhere on your system drive.

Essential Step: check here and make sure you download and install the most up-to-date version where the required file is e.g. VV_SR_2021_2.tar and the numbers indicate the creation date i.e. 2021_02 = February 2021

$ mkdir /path/to/seqrepo
$ cd /path/to/seqrepo
$ wget https://www528.lamp.le.ac.uk/vvdata/vv_seqrepo/VV_SR_20xx_xx.tar
$ tar -xvf VV_SR_20xx_xx.tar
$ rm VV_SR_20xx_xx.tar

where /path/to/seqrepo should be where you install the database e.g. /Users/Shared/seqrepo_dumps/ or /local/seqrepo

Setting up VVTA database (PostGreSQL >=10.5)

You will need to install a local version of the VVTA database.

First create the database and a user account:

psql
CREATE ROLE <USER> WITH CREATEDB;
ALTER ROLE <USER> WITH LOGIN;
ALTER ROLE <USER> WITH PASSWORD '<password>';
CREATE DATABASE vvta WITH OWNER=<USER> TEMPLATE=template0;

Where:

  • <USER> should be a user-name e.g. uta_admin
  • password is a unique password for user

To fill this database, download the gzipped uta genetics database, and upload it into psql.

Essential Step: check here and make sure you download and install the most up-to-date version

Postgres < version 14.0

$ wget --output-document=VVTA_202x_xx.noseq.psql.gz https://www528.lamp.le.ac.uk/vvdata/vvta/VVTA_202x_xx.noseq.psql.gz
$ gzip -cdq VVTA_202x_xx.noseq.psql.gz | psql -U <USER> -v ON_ERROR_STOP=0 -d vvta -Eae

Postgres >= version 14.0

$ wget --output-document=VVTA_202x_xx.noseq.psql.gz https://www528.lamp.le.ac.uk/vvdata/vvta/VVTA_202x_xx.noseq.psql.gz
$ gzip -cdq -k VVTA_202x_xx.noseq.psql.gz | sed 's/anyarray/anycompatiblearray/g' | psql -U <USER> -v ON_ERROR_STOP=0 -d vvta -Eae

Configuration

Before using VariantValidator some configuration is required, as described in the Manual.

Developers

To work on the VariantValidator code, you'll need to install additional dependencies and install VariantValidator in an editable manner. Tests can be run using PyTest.

cd variantValidator/
pip install -r requirements.txt
pip install -r requirements_dev.txt
pip install -e .
pytest

Please make all Pull Requests to the develop branch. Id you are unsure, contact admin via issues