Installation of WhatsHap is easiest if you use Conda.
Installation with Conda¶
First, ensure you have Conda (miniconda or Anaconda) installed and made the proper settings to enable the “bioconda” channel. For that, follow the bioconda installation instructions.
Then WhatsHap can be installed with this command:
conda install whatshap
For a smaller download and installation size, add
nomkl to this command.
This will avoid installing the (quite large) “Intel Math Kernel Library”,
which WhatsHap does not use anyway:
conda install whatshap nomkl
Installation with pip¶
Before you can pip install, you need to install dependencies that pip cannot
install for you. WhatsHap is implemented in C++ and Python. You need to have a
C++ compiler, Python 3.3 (or later) and the corresponding Python header files.
Python 3.5 is slightly faster than 3.4. In Ubuntu, installing the packages
python3-dev will take care of all required
WhatsHap can then be installed with pip:
pip3 install --user whatshap
This installs WhatsHap into
$HOME/.local/bin. Then add
$HOME/.local/bin to your
$PATH and run the tool:
export PATH=$HOME/.local/bin:$PATH whatshap --help
Alternatively, you can also install WhatsHap into a virtual environment if you are familiar with that.
Installing an unreleased development version¶
If you for some reason want to use the most recent development version of
WhatsHap, you can install it in the following way. These instructions will
create a virtual environment in the directory
whatshap-env that contains
WhatsHap. Simply delete that directory to uninstall the software. Other WhatsHap
versions you may have installed in other locations remain unaffected.
python3 -m venv whatshap-env whatshap-env/bin/pip install --upgrade pip whatshap-env/bin/pip install git+https://bitbucket.org/whatshap/whatshap
You can then run WhatsHap like this:
You should see a version number like
0.18.dev119+g5ba23de, which means that
this is going to become version 0.18, with 119 commits ahead of the previous