THIS REPO IS IN ACTIVE DEVELOPMENT.
SOME MODIFICATIONS SOME MORE MODIFICATIONS MORE MODIFICATIONS
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
- lsb_release:
RedHat/CentOS:
- Create a new database named "relecov" (this is mandatory)
- Create a new user with permission to read and modify that database.
- Write down user, passwd and db server info.
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
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
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".
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.
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
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
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
Relecov usage documentation is included in the platform.
In the menu, click on Documentation.