Anfisa

• Anfisa
  • Overview
  • Online Development Documentation
  • Public Demo
  • Installation
    • Select branch or release:
    • Installation instructions
      • Installing via Docker
      • Installing without Docker
    • Ingesting demo whole genome

Overview

Anfisa is a Variant Analysis and Curation Tool. Its purpose is to bring together Genetic Research and Clinical settings and provide a medical geneticist with access to research Genome.

See more about the goal of the project at https://forome.org/

Online Development Documentation

• Installation & Administration Documentation

https://foromeplatform.github.io/documentation/anfisa-dev.v0.7/

• User Documentation

https://foromeplatform.github.io/documentation/anfisa-user.v0.7/

Public Demo

For a quick introduction, look at a demo of Anfisa based on a high confidence small variants callset v 4.2 created by NIST by integrating results of sequencing, alignment and variant calling from different sources; including both short and long read techniques.

The demo server with REST API and a stable built-in UI is available at: https://api.demo.forome.org/

A novel React Front End is under development and a beta version can be previewed at: https://app.demo.forome.org/

Installation

Select branch or release:

This is a master branch that from time to time can be unstable or untested. If you would like to try Anfisa, we strongly recommend installing it from one of the released tags

Installation instructions

To install Anfisa on a local Linux or MacOS system:

1. Clone the repository on your system. We suggest cloning one of the tagged (released) version as the master branch is undergoing continues development.

       git clone https://github.com/ForomePlatform/anfisa.git

2. Change into anfisa directory, e.g.:

       cd anfisa

3. Checkout to stable release (for ex this is latest release in github)

       git checkout v.0.7.8

4. Decide what directory will be a working directory for Anfisa

5. Decide which of the following installation paths you prefer:

• Use a Docker container. This method will also install Druid and other dependencies. However, Druid requires at least 8G of memory, if your box does not have this amount of RAM, you should avoid running Druid or adjust its settings. Druid can also be run on a separate box.
• Install all components in your local system. This is only recommended if you will contributing to Anfisa development or customizing its code.

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Installing via Docker

*Install Anfisa in Docker

Installation instructions for docker-compose you can find here

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Installing without Docker

Ensure that the following packages are installed on your system:

• curl
• zip
• unzip
• python3-dev
• python3-pip
• python3-venv
• MongoDB

Note: pip3 version should be 3.9 or higher

Click on the below appropriate tab to install the required packages on Ubuntu or Mac OS.

Install prerequisites on Ubuntu

1. The following command can be used to install required packages:

   sudo apt update && sudo apt install zip unzip python3-dev python3-pip python3-venv curl
   

   You might need to restart your shell or source .bashrc (or similar) file after the installation

   To install MongoDB follow the link Install MongoDB Community Edition on Ubuntu.

2. [Optionally] Create virtual environment and activate it. We will be installing a lot of dependent packages, make sure you have permission to do it. A sample command is:

   python3 -m venv .anfisa && source .anfisa/bin/activate
   

3. Make sure MongoDB is running. The command can be used:

   sudo systemctl status mongod
   

If its endpoint is not localhost:27017, you will need to edit anfisa.json.

4. Make sure that sphinx is installed. The installation command is:

   sudo apt-get install python3-sphinx
   

Install prerequisites on Mac OS

1. Install Homebrew Package Manager, command can be used:

   /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
   

   Run the following command to install required packages:

   xcode-select --install
   brew update
   brew install curl
   brew install zip
   brew install unzip
   

   To install MongoDB follow the link Install MongoDB Community Edition on macOS.

2. [Optionally] Create virtual environment and activate it. We will be installing a lot of dependent packages, make sure you have permission to do it. A sample command is:

   python3 -m venv .anfisa && source .anfisa/bin/activate
   

3. Make sure MongoDB is running, use link Install MongoDB Community Edition on macOS to verify that MongoDB is running accroding to the choosen running option. If its endpoint is not localhost:27017, you will need to edit anfisa.json.

4. Make sure that sphinx is installed. The installation command is:

   brew install sphinx-doc
   

Install Anfisa

First, the script will ask for an installation directory. By default it would install in the same directory where you have cloned the code, but you can change it to any other directory. Once installation directory is confirmed, the script will configure Anfisa for your local system.

1. Run deploy script (will use pip to install requirements):

   ./deploy_local.sh
   

2. When the script has finished, it will display the command to start Anfisa server, for example:

env PYTHONPATH=. python3 app/run.py <Absolute path to the chosen working directory>/anfisa_hostname.json

3. When the system is running you can access the web interface by the url: http://localhost:8190/dir

The port is configurable in your configuration file. Configuration file is located in the selected working directory with the name:

anfisa_hostname.json

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Ingesting demo whole genome

You will need approximately 25G of space available to experiment with a whole genome

• First, download prepared dataset
• Unpack the content into some directory (e.g. directory data under your work directory)
• Run Anfisa ingestion process

Here are sample commands that can be executed:

curl -L -O https://forome-dataset-public.s3.us-south.cloud-object-storage.appdomain.cloud/pgp3140_wgs_nist-v4.2.tar.gz

docker cp pgp3140_wgs_nist-v4.2.tar.gz anfisa-backend:/anfisa/a-setup/data/examples/
docker exec -it anfisa-backend sh -c 'cd /anfisa/a-setup/data/examples && tar -zxvf pgp3140_wgs_nist-v4.2.tar.gz'
docker exec -it anfisa-backend sh -c 'PYTHONPATH=/anfisa/anfisa/ python3 -u -m app.storage -c /anfisa/anfisa.json -m create --reportlines 1000 -f -k xl -i /anfisa/a-setup/data/examples/pgp3140_wgs_nist-v4.2/pgp3140_wgs_nist-v4.2.cfg XL_PGP3140_NIST_V42'