The simplest way to run mity
is via docker
:
docker run drmjc/mity -h
If you have freebayes
>=1.2 and Brent Pederson's gsort
installed, then pip
should work well.
pip3 install mitywgs
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 withpython3-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