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INSTALL

Installing via Docker

The simplest way to run mity is via docker:

docker run drmjc/mity -h

Installing via pipx

If you have freebayes >=1.2 and Brent Pederson's gsort installed, then pipx should work well.

pipx install mitywgs

If you encounter any issues, check to see if you have all the necessary packages installed (see Manual installation for more details).

Manual installation

Install homebrew (skip if you have already installed homebrew):

sh -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)"
export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH

Install dependencies:

sudo apt-get install -y make build-essential libssl-dev zlib1g-dev libbz2-dev \
  libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev \
  xz-utils tk-dev libffi-dev liblzma-dev python3-openssl git

Note that python-openssl has been replaced with python3-openssl

Upgrade pip and export path:

pip3 install --upgrade pip
export PATH=$PATH:.local/bin:$HOME/.pyenv/versions/3.7.4/bin

Install dependencies: freebayes (>=1.2.0), htslib (tabix+bgzip), gsort and tabix:

brew tap brewsci/bio
brew install freebayes
brew install htslib
sudo apt-get install -y tabix

curl -s https://api.github.com/repos/brentp/gsort/releases/latest \
  | grep browser_download_url \
  | grep -i $(uname) \
  | cut -d '"' -f 4 \
  | wget -O gsort -qi -
chmod +x gsort
export PATH=.:$PATH

Install mity globally with:

pipx install mitywgs

Or install with a python virtual environment.