# rari is not on pypi:
pip3 install git+https://github.com/nredell/rari
pip3 install git+https://github.com/smautner/natto.git
lapsolver should not be required anymore...
# lapsolver needs cmake and this seems to work
conda install cmake pip make gxx_linux-64 gcc_linux-64 fish
export CMAKE_MAKE_PROGRAM=$(which make)
export CC=$(which x86_64-conda_cos6-linux-gnu-gcc)
export CXX=$(which x86_64-conda_cos6-linux-gnu-g++)
running natto
importnattoasna# input is a pair of scanpy-anndata objects# 'natto.input.load' constructs anndata objects from multiple formatsadata_1, adata_2=na.l.loadimmune(subsample=250)
# preprocessing and clusteringdata=na.prepare(adata_1,adata_2)
# similarity measureprint("similarity:",na.similarity(data))
# EM algorithm and plottingna.tunnelclust(data)
na.drawpair(data, tunnellabels=True)