Core dependencies include:

  • Cellranger (from 10X Genomics) >= 6.0

  • Python3

  • The cgat-core pipeline framework

  • Python packages as per python/requirements.txt

  • R >= 4.0

  • Various R libraries (see R/install.packages.R)

  • Latex

  • The provided cellhub R library

Optional dependencies include:

  • CellBender

  • GMM-Demux

  • pegasuspy (for demuxEM)


  1. Install the cgat-core pipeline system following the instructions here

  2. Clone and install the cellhub-devel repository e.g.

git clone
cd cellhub
python develop


Running “python develop” is necessary to allow pipelines to be launched via the “cellhub” command.

  1. In the same virtual or conda environment as cgat-core install the required python packages:

    pip install -r cellhub/python/requirements.txt
  2. To install the required R packages (the “BiocManager” and “devtools” libraries must be pre-installed):

    Rscript cellhub/R/install.packages.R
  3. Install the cellhub R library:

    R CMD INSTALL R/cellhub


On some systems, automatic detection of the HDF5 library by the R package “hdf5r” (a dependency of loomR) is problematic. This can be worked around by explicitely passing the path to your HDF5 library h5cc or h5pcc binary, e.g.

install.packages("hdf5r", configure.args="--with-hdf5=/apps/eb/dev/skylake/software/HDF5/1.10.6-gompi-2020a/bin/h5pcc")