covidapp

Transmission Trend Similarity Network Analysis Tool

Requirements

The covidapp is tested working in Mac OS and Debian Linux systems
covidapp needs the following to run successfully;

1. R - https://cloud.r-project.org/
   Download, install and test to make sure you have the latest version of R. You can check for your R install using the below command
   

R --version

2. Cytoscape - https://cytoscape.org/download.html
   Download, install and test to make sure you have the latest version of R
   Make sure to note the cytoscape installation folder
   
   
3. Java
   Current cytoscpae version needs Java Runtime Environment of 1.8. Make sure you have the correct JVM and that it is in the system path. You can use the below command to check for your JAVA_HOME location
   

echo $JAVA_HOME

4. PHP
   Make sure you have a working PHP installation
   You can use the below command to check for PHP
   

php -v

5. Xterm
   If its not already available, please install xquartz for mac, to use the xterm in Mac OS.
   In the debian linux, you can install xterm using the below command;
   

sudo apt install xterm

Usage

1. Download
   If you have git installed in your system, clone the covidapp github repo using the below command;
   

git clone https://github.com/bioinfoacademy/covidapp.git

You can also just download the project folder as a zip file and unzip it.
2. Configure
From the project 'covidapp' folder, open the config.txt file and edit it to have the correct path for cytoscape.sh, input data file, jdk-path and the attributes file. You could use the example data files in the project 'data' folder to test the app. You can also use the example data files to format your own data files.

3. Running
With the config.txt file fixed, change to your covidapp directory and run the script using the below command;

bash covid-pipeline.sh

4. Results
The resulting tree image and the network image are written to the covidapp/images folder

Contributions

Please fork this project, retweek it for your own analysis, publish results, alert relevant officials and save lives.

Errors

If you need any help reproducing the test data analysis or retweeking it to fit your own dataset, please feel free to submit an issue in this repository.