punkst

punkst is an ongoing effort to implement scalable tools for analyzing high resolution spatial transcriptomics data.

It includes a new implementation of FICTURE to replace the python package

Documentation: https://Yichen-Si.github.io/punkst

Installation

See more details in install page.

If you have difficulty installing, let us known (by opening an issue). You can also try Docker (see below), but the Docker image is not always up to date.

Building from Source

Prerequisites

• Git
• CMake: 3.15 to 3.23
• C++17 compiler* (GCC ≥8, Clang ≥5, MSVC 2017+)
• TBB, OpenCV

*We do assume your compiler properly supports C++17. Consider updating the compiler if you encounter issues.

# 1) Clone the repository
git clone --recursive https://github.com/Yichen-Si/punkst.git
cd punkst
# 2) Create and enter a build directory
mkdir build && cd build
# 3) Configure
cmake ..
# 4) Build
cmake --build . --parallel # or make

If you did not clone the submodule (Eigen) initially, you can do

git submodule update --init

If TBB is not found, you can install it by sudo apt-get install libtbb-dev or yum install tbb-devel on linux and brew install tbb on macOS.

If you don't have root access on linux, you can install oneTBB locally.

If you installed some dependencies locally, you may need to specify their paths like

cmake .. \
  -DOpenCV_DIR=$HOME/.local/lib/cmake/opencv4 \
  -DTBB_DIR=$HOME/user/opt/tbb/lib/cmake/tbb \
  -DCMAKE_PREFIX_PATH="$HOME/.local"

The punkst binary will be placed in bin/ under the project root.

Verify the Build

punkst/bin/punkst --help

You should see a message starting with

Available Commands
The following commands are available:

Using Docker

Prerequisite: Docker

docker pull philo1984/punkst:latest

Viirfy the installation:

docker run --rm philo1984/punkst:latest punkst --help