Installation
Dependencies
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)
Installation
Install the cgat-core pipeline system following the instructions here https://github.com/cgat-developers/cgat-core/.
Clone and install the cellhub-devel repository e.g.
git clone https://github.com/sansomlab/cellhub.git
cd cellhub
python setup.py develop
Note
Running “python setup.py develop” is necessary to allow pipelines to be launched via the “cellhub” command.
In the same virtual or conda environment as cgat-core install the required python packages:
pip install -r cellhub/python/requirements.txt
To install the required R packages (the “BiocManager” and “devtools” libraries must be pre-installed):
Rscript cellhub/R/install.packages.R
Install the cellhub R library:
R CMD INSTALL R/cellhub
Note
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")