SCENIC+

Installation

①首先将这五个包在github上下载并上传至服务器~/packgae_python

②安装代码

cd /public/home/chenzhh/packgae_python

mamba create -n Mujigae python=3.11.8 -y
mamba activate Mujigae

mamba install -y -c conda-forge -c bioconda python-annoy pybedtools pybigwig pybigtools pysam macs2 bedtools python-igraph leidenalg pytables scatac-fragment-tools
#pip编译困难包↑

grep -Ev 'git\+https://github.com/aertslab/|^(annoy|pybedtools|pyBigWig|pybigtools|pysam|macs2|igraph|leidenalg|tables|scatac-fragment-tools)==' \
  scenicplus/requirements.txt > /tmp/scenicplus.req


python -m pip install -U pip "setuptools==79.0.1" wheel setuptools-scm
python -m pip install -r /tmp/scenicplus.req

#  python -m pip install --force-reinstall "igraph==0.11.4" "leidenalg==0.10.2" "pybedtools==0.9.1" "pybigtools==0.1.2" "pysam==0.22.0" "tables==3.9.2" --no-deps

python -m pip install --no-deps ./pySCENIC ./LoomXpy ./pycistarget ./pycisTopic ./scenicplus

③验证

python - <<'PY'
import scenicplus, pycisTopic, pycistarget, pyscenic, loomxpy
print("SCENIC+ install OK")
PY

④后续

mamba install ipykernel
python -m ipykernel install --user --name=mujigae --display-name "Mujigae Py311"