FROM condaforge/mambaforge

LABEL maintainer="Jan Detleffsen <[email protected]>"

COPY . /home/sc_framework/

COPY scripts /scripts/

# Set the time zone (before installing any packages)

RUN echo 'Europe/Berlin' > apt-get install -y tzdata

# make scripts executeable

RUN chmod +x scripts/bedGraphToBigWig

# Clear the local repository of retrieved package files

RUN apt-get update --assume-yes && \

apt-get clean

# install Fortran compiler

RUN apt-get install --assume-yes gfortran

# Set timezone for tzdata

ARG DEBIAN_FRONTEND=noninteractive

ENV TZ=Etc/UTC

# Install missing libraries

RUN apt-get install bedtools && \

apt-get install -y libcurl4 && \

apt-get install -y git && \

apt-get install -y build-essential && \

pip install --upgrade pip

# update mamba

RUN mamba update -n base mamba && \

mamba --version

# install enviroment

RUN mamba env update -n base -f /home/sc_framework/sctoolbox_env.yml

# prevent "Build failed for the C core of igraph." #400

RUN mamba install -y "louvain>=0.8.2"

# install sctoolbox

RUN pip install "/home/sc_framework/[core,downstream]" && \

pip install pytest && \

pip install pytest-html && \

pip install pytest-cov && \

pip install pytest-mock

# Generate an ssh key

RUN apt-get install -y openssh-client && \

mkdir .ssh && \

ssh-keygen -t ed25519 -N "" -f .ssh/id_ed25519