Dockerfile_pip

FROM jsschrepping/r_docker:jss_R432_bioc318

MAINTAINER Jonas Schulte-Schrepping (jsschrepping)

###################
### INSTALL PIP ###

# update pip
RUN pip3 install --upgrade pip

# install 
RUN pip3 install numpy==1.26.4
RUN pip3 install pandas==2.2.1
RUN pip3 install scipy==1.12.0
RUN pip3 install scikit-misc==0.3.1

RUN pip3 install MACS3==3.0.1
RUN pip3 install scanpy==1.10.0
RUN pip3 install scvelo==0.3.2
RUN pip3 install velovae==0.1.2
RUN pip3 install cellrank==2.0.3
RUN pip3 install scFates==1.0.7
RUN pip3 install scrublet==0.2.3
RUN pip3 install cellphonedb==5.0.0
RUN pip3 install decoupler==1.6.0
RUN pip3 install omnipath==1.0.8
RUN pip3 install harmonypy==0.0.9  
RUN pip3 install muon==0.1.6

RUN pip3 install gdown==5.1.0 
RUN pip3 install wget==3.2

############
### TEST ###

# list pip packages
RUN python3 -m pip list > /logs/log_install_pip.txt