Operating system(s): Ubuntu 20.04 and 22.04.
Programming language used: Bash
Important: Check bash in your linux using the command:
which bash
Desired output:
/usr/bin/bash
Other requirements: Java 11, Python3, GLIBC 2.28 or higher.
Executable Binaries are converted from bash using Shell Script Compiler (SHC).
Developer: Ranjan Jyoti Sarma and Prof. N. Senthil Kumar
i. Install git using:
sudo apt -y install git
ii. Change the current directory to Desktop:
cd ~/Desktop
iii. Download WEAP using git:
git clone https://github.com/ranjanjs34/weap.git
iv. After downloading, enter into the WEAP:
cd WEAP
NOTE: Advanced users may keep WEAP in any convenient location.
Add execution permission to binary files configure and reference:
sudo chmod +x ./configure
sudo chmod +x ./reference
To download the prerequisite tools, run the configure as :
./configure
Enter the directory address where it downloads the pre-requisite tools: for example: /home/$USER/Desktop
There should not be any ‘/’ at the end of the directory address.
This Script will automatically download and install the required tools and will add to the path so that WEAP can recognize the internal commands. As ANNOVAR cannot be distributed, users need to download the ANNOVAR from the ANNOVAR website after registration. Please download the ANNOVAR from https://www.openbioinformatics.org/annovar/annovar_download_form.php manually by registering, unzip and keep it in Tool directory as 'annovar'.
./reference
This will download the reference genome, Variants with Allele frequency from genomAD project, dbSNP data from gatk bundle and datasets from ANNOVAR web resource to annotate the variants.
There should not be any ‘/’ at the end of the input and output directory address.
./WEAP