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Installation
If you want to install MUSET using conda or building from sources, GGCAT should be installed separately. If you want to create a Singularity image, you can skip this part.
To build GGCAT you will first need the Rust stable (>= 1.75) toolchain. It can be downloaded with the following commands:
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
rustup toolchain install stable
Then GGCAT can be installed with the commands:
git clone https://github.com/algbio/ggcat --recursive
cd ggcat/
cargo install --path crates/cmdline/ --locked
which put the ggcat binary in the directory $HOME/.cargo/bin.
To launch the tool directly from the command line, verify that the above directory has been added to your $PATH environment variable.
Requirements:
You can install muset by creating a conda environment:
git clone --recursive https://github.com/camiladuitama/muset.git
cd muset
conda env create -n muset --file environment.yaml
To run muset remember to activate the conda environment with:
conda activate muset
You can check if muset is correctly installed as follows:
cd test
muset fof.txt
Build requirements:
- a recent version of GCC (or clang) that supports the C++17 standard
- cmake >= 3.15
Additional dependencies:
To clone the repository:
git clone --recursive https://github.com/camiladuitama/muset.git
To build the tool:
cd muset
mkdir build && cd build
cmake ..
make
Executables will be made available in the bin sub-directory relative to the root folder of the repository.
To make the muset command available, remember to include the absolute path of MUSET's executables in your PATH environment variable, e.g., adding the following line to your ~/.bashrc file:
export PATH=/absolute/path/to/muset/bin:${PATH}
You can check if muset is correctly installed as follows:
cd test
muset fof.txt
Requirements:
- Singularity installed on your system. Refer to the Singularity Installation Guide for detailed instructions.
To build a singularity image (e.g., muset.sif):
git clone --recursive https://github.com/CamilaDuitama/muset.git
cd muset/singularity
sudo singularity build muset.sif Singularity.def
To run muset and see the help message, use the following command:
singularity exec /path/to/muset.sif muset -h'
To try muset with example data, run it from the test directory within the repository as follows:
singularity exec /path/to/muset.sif muset fof.txt'