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Requirements

Dependencies

Building and running the cmuts pipeline requires the following packages:

Required:

  • python>=3.9 with all packages in requirements.txt
  • cmake>=3.29 with pkg-config
  • autoconf, automake, libtool
  • samtools and htslib
  • hdf5
  • fastp

Optional:

  • omp — enables multithreaded pairwise counting (builds fine without it)

The MPI build also requires:

  • openmpi
  • hdf5-mpi

Demultiplexing with cmuts align requires:

  • ultraplex

Note that ultraplex requires python==3.9, and will not install for more recent versions of python.

The following should install all (save for python and its packages) on a personal device. For installation on a managed cluster, consult the respective guidelines.

# Install brew from https://brew.sh
# Required:
brew install cmake autoconf automake libtool samtools
brew install hdf5       # for non-MPI builds
# Optional:
brew install libomp     # enables multithreaded pairwise counting
# For MPI builds only:
brew install openmpi hdf5-mpi

sudo apt-get update
# Required:
sudo apt-get install -y cmake autoconf pkg-config
sudo apt-get install -y samtools libhts-dev
sudo apt-get install -y libhdf5-dev
# Optional:
sudo apt-get install -y libomp-dev   # multithreaded pairwise counting
# For MPI builds only:
sudo apt-get install -y libopenmpi-dev openmpi-bin
sudo apt-get install -y libhdf5-openmpi-dev

# Required:
sudo dnf install -y cmake autoconf pkg-config
sudo dnf install -y samtools htslib-devel
sudo dnf install -y hdf5-devel
# Optional:
sudo dnf install -y libomp-devel     # multithreaded pairwise counting
# For MPI builds only:
sudo dnf install -y openmpi-devel hdf5-openmpi-devel
# Load MPI module (may be required):
module load mpi/openmpi-x86_64

Verify Dependencies

Run these commands to verify the dependencies are successfully installed: 

cmake --version
pkg-config --modversion hdf5
autoreconf --version
samtools --version
h5ls --version
For MPI builds, also run: 
mpirun --version

Python Dependencies

To create a conda environment with all required dependencies, you may run

conda create -n cmuts python=3.9
conda activate cmuts
pip3 install -r requirements.txt
conda install -c bioconda fastp

For the cmuts align dependencies required for demultiplexing, also run

conda install -c bioconda ultraplex

HDF5 Configuration

If cmake has trouble finding your HDF5 installation, you can set

export HDF5_DIR=/path/to/hdf5/installation

If installed via brew, the command brew info hdf5 may be helpful for finding the desired path.

On Linux, HDF5 is typically installed to /usr/lib/x86_64-linux-gnu/hdf5 (Debian/Ubuntu) or /usr/lib64 (Fedora/RHEL). You can find it with:

pkg-config --variable=libdir hdf5