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INSTALL.md

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INSTALL

Installing via Docker

The simplest way to run mity is via docker:

docker run drmjc/mity -h

Installing via Pip

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

pip3 install mitywgs

Manual Installation

All of these commands are available as

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:

export PYTHONPATH=/usr/local/lib/python3.7/dist-packages:/usr/lib/python3/dist-packages
pip3 install mitywgs

Or install with a virtual environment:

sudo apt-get install python3-venv
unset PYTHONPATH
python3 -m venv .
source bin/activate
./bin/pip install wheel
./bin/pip install mitywgs