Installation

UShER package can be installed using three different options: (i) conda, (ii) Docker and (iii) installation scripts, as described below.

Conda

A quick method is via conda:

# Create a new environment for UShER
conda create -n usher-env
# Activate the newly created environment
conda activate usher-env
# Set up channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
# Install the UShER package
conda install usher

Conda Local Build

git clone https://github.com/yatisht/usher.git
cd usher/install
conda env create -f environment.yml
conda activate usher
cd ..
mkdir build
cd build
git clone https://github.com/oneapi-src/oneTBB
cd oneTBB
git checkout cc2c04e2f5363fb8b34c10718ce406814810d1e6
cd ..
cmake  -DTBB_DIR=${PWD}/oneTBB  -DCMAKE_PREFIX_PATH=${PWD}/oneTBB/cmake ..
make -j
cd ..

followed by, if on a MacOS system:

rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/macOSX.x86_64/faToVcf .
chmod +x faToVcf
mv faToVcf scripts/

or if on a Linux system:

rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/faToVcf .
chmod +x faToVcf
mv faToVcf scripts/

Executables will be located in the build and scripts directories. Make sure they’re on your path for your system as appropriate, or that you modify your commands to indicate their location.

export PATH=$PATH:/path/to/install/usher/build/
export PATH=$PATH:/path/to/install/usher/scripts/

Docker

From DockerHub:

docker pull pathogengenomics/usher:latest
docker run -t -i pathogengenomics/usher:latest /bin/bash

OR locally:

git clone https://github.com/yatisht/usher.git
cd usher
docker build --no-cache -t usher install/
docker run -t -i usher /bin/bash

Installation scripts

git clone https://github.com/yatisht/usher.git
cd usher

For MacOS 10.14 or above:

./install/installMacOS.sh

For Ubuntu 18.04 and above (requires sudo privileges):

./install/installUbuntu.sh

For CentOS 7 and above (requires sudo privileges):

./install/installCentOS.sh