Installation¶
Supported platforms¶
| Platform | Environment |
|---|---|
| Linux x86-64 | Python 3.10 or later |
| Windows (WSL2) | Linux Python 3.10 or later inside WSL2 |
BSReadSim supports Linux x86-64 and Windows through WSL2. Native Windows, macOS, and Linux ARM64 are not currently supported.
Install from Bioconda¶
Coming soon
Bioconda installation is coming soon. It's the recommended installation method, especially on shared systems and HPC clusters.
Install from source¶
Requirements¶
The following dependencies are needed to build BSReadSim from source.
- Python 3.10 or later
- GCC or Clang with C++17 support
- CMake 3.20 or later
- GNU Make, Autoconf, and zlib
Choose one of the following ways to prepare an isolated build environment.
Using Conda or Mamba
Conda can provide the compilers, libraries, and Python environment in user space without administrator access:
conda create -n bsenv -c conda-forge \
python pip cmake c-compiler cxx-compiler make autoconf zlib git
conda activate bsenv
mamba can be used in place of conda.
Using venv with system tools
venv isolates the Python packages; the build tools must be installed on
the system or made available separately.
On Ubuntu or WSL2 with sudo access, install the required tools with:
sudo apt-get update
sudo apt-get install --yes \
autoconf build-essential cmake git python3-dev python3-venv zlib1g-dev
On HPC or shared server without sudo access, load or install the dependencies in your user environment first, then create and activate the virtual environment:
If the virtual environment was created with HPC modules, load the same modules before activating it in future sessions or batch jobs.
Build and install¶
With the selected environment active, clone the repository and install BSReadSim:
# For Conda: conda activate bsenv
# For venv: source bsenv/bin/activate
git clone --recurse-submodules https://github.com/wbvguo/BSReadSim.git
cd BSReadSim
python -m pip install .
Verify the installation¶
Check the installed version with: