Install

Install pod5

The most recent release of the pod5 package can be installed using pip

$ pip install pod5

This package depends upon lib_pod5 which provides the OS-dependent C++ pod5 library. The lib_pod5 package will be installed automatically py pip and as such, common OS platforms and should work out of the box.

Installation from Source

If you want to contribute to pod5 or if our pre-built binaries do not meet your platform requirements, you can build pod5 from source using the instructions below.

Developing with Conan

For this development process you will need conan installed. You can install conan<2 using pip or your platforms’ package manager (e.g. brew) You will also need the python setuptools_scm package to manage pod5 versioning:

# Conan and python build dependencies
$ pip install "conan<2" build
$ conan --version
Conan version 1.48.0

# Get the repo and submodules
$ git clone https://github.com/nanoporetech/pod5-file-format.git
$ cd pod5-file-format
$ git submodule update --init --recursive

# Creates _version.py and cmake/POD5Version.cmake which are ignored by git
$ pip install setuptools_scm
$ python -m setuptools_scm
$ python -m pod5_make_version

# Install libs for a Release build using the system default compiler + settings:
# Note the build=missing, will build any libs not available on your current platform as binaries:
$ mkdir build
$ cd build
$ conan install --build=missing -s build_type=Release .. && cmake -DENABLE_CONAN=ON -DCMAKE_BUILD_TYPE=Release .. && make -j

Arm 64 MacOS Builds

Note

On OSX arm builds, an extra argument may be needed to make cmake build an arm64 build on all OSX platforms:

$ cmake -DENABLE_CONAN=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_ARCHITECTURES=arm64 ..

Developing

Building the project requires that several tools and libraries are available

$ sudo apt install -y -V ca-certificates lsb-release wget
$ wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
$ sudo apt install -y -V ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
$ sudo apt update

# Now install the rest of the dependencies:
$ sudo apt install cmake libzstd-dev libzstd-dev libboost-dev libboost-filesystem-dev libflatbuffers-dev

# Finally start build of POD5:
$ git clone https://github.com/nanoporetech/pod5-file-format.git
$ cd pod5-file-format
$ git submodule update --init --recursive
$ mkdir build
$ cd build
$ cmake ..
$ make -j

Python Development Setup

After completing the required build stages above, to create a Python virtual environment for development use the Makefile in the python directory to install the two pod5 python packages including all dev dependencies such as pre-commit and black.

$ cd python
$ make install

Note this will completely clean the existing python virtual environment. If one only requires an update to the python environment entry-points (e.g. pod5 inspect) simply run:

$ make update

Installing Pre-commit Hooks

The project uses pre-commit to ensure code is consistently formatted, you can set this up using pip but if you chose to use the supplied Makefile this will be done automatically as detailed above

$ cd pod5-file-format

# Install pre-commit hooks in your pod5-file-format repo:
$ pip install pre-commit==v2.21.0
$ pre-commit install

# Run hooks on all files:
$ pre-commit run --all-files