relecov-platform

THIS REPO IS IN ACTIVE DEVELOPMENT.

Table of contents

• Installation
• Upgrade new release
• Documentation

Installation

Relecov docker installation

SOME MODIFICATIONS SOME MORE MODIFICATIONS MORE MODIFICATIONS

Install relecov-platform in your server (RedHat / CentOs / Ubuntu)

Before starting the installation check :

• You have sudo privileges to install the additional software packets that relecov-platform needs.
• Database (MySQL/MariaDB) is running
• Local server configured for sending emails
• Apache server is running on local server
• Dependencies:
  • lsb_release: RedHat/CentOS: yum install redhat-lsb-core

Create relecov database and grant permissions

1. Create a new database named "relecov" (this is mandatory)
2. Create a new user with permission to read and modify that database.
3. Write down user, passwd and db server info.

Clone github repository

Open a linux terminal and move to a directory where relecov code will be downloaded

cd <your personal folder>
git clone https://github.com/BU-ISCIII/relecov-platform.git relecov-platform
cd relecov_platform

Configuration settings

Copy the initial setting template into a file named install_settings.txt

cp conf/template_install_settings.txt initial_settings.txt

Open with your favourite editor the configuration file to set your own values for database ,email settings and the local IP of the server where relecov-platform will run.

sudo nano install_settings.txt

Run installation script

Relecov-platform is installed on the "/opt" directory. Before start the installation be sure you have sudo priveleges.

Execute the following commands in a linux terminal.

sudo bash install.sh

After installation is completed open you navigator typing "localhost" or the "server local IP".

Install nextstrain

The Nextstrain CLI ties together all necesary pieces to provide a consistent way to run pathogen workflows, access Nextstrain tools like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch, and publish datasets to nextstrain.org.

Download installer

Move to the installation path and download installer

mkdir -p /opt/nextstrain
cd /opt/nextstrain
curl -fsSL --proto '=https' https://nextstrain.org/cli/installer/linux > nexstrain_installer_$(date "+%Y%m%d").sh

Set NEXSTRAIN_HOME env variable and run installer

export NEXTSTRAIN_HOME=/opt/nextstrain
bash nexstrain_installer_$(date "+%Y%m%d").sh

Set conda as default run-time.This will install the nexstrain conda env with all deps using micromamba.

/opt/nextstrain/cli-standalone/nextstrain setup --set-default conda

Copy service file to /usr/lib/systemd/system

cp ./conf/nextstrain.service /etc/systemd/system

Copy auspice dataset to datasets folder. This contains all the data that should be rendered by nextstrain app. This is created using the nexstrain_relecov workflow

mkdir -p /opt/nextstrain/dataset/sars-cov-2
cp -r /path/to/auspice /opt/nextstrain/dataset/sars-cov-2

Upgrade to new release

Update github repository

Open a linux terminal and move to a directory where relecov code was download during installation

cd < folder where relecov code was download >
git pull
cd relecov_platform

Run upgrade script

Execute the following command in a linux terminal. After the code is updated, the script requests you enter the sudo password to restart Apache server to update changes.

bash install.sh --upgrade

Documentation

Relecov usage documentation is included in the platform.

In the menu, click on Documentation.