[Python] Impossible to install python deps with conda using bash script

tried writing a script to aumatically download and install some dependencies i need.

Is not possible to install such dependencies directly i already tried and it istalls the wrong version which is incompatible with my code

when i try to execute the script inside the container worked without a fuss

the script is compile.sh

dockerfile:

FROM mambaorg/micromamba:2.3.1-ubuntu24.10
USER root
RUN apt-get update && apt-get install -y \
build-essential \
curl \
wget \
nano \
git \
tcsh\
ninja-build \
meson

COPY ./app /home/screener
WORKDIR /home/screener/install
RUN chmod +x ./compile.sh

WORKDIR /home/screener
#create env from screener-lock #-f /home/screener/app/env/screener.yml
RUN micromamba create -n Screener -f ./env/screener.yml
RUN micromamba run -n Screener pip install --upgrade pip

USER $MAMBA_USER

#RUN micromamba install -n Screener <chem_data package>
#RUN micromamba env -n Screener export > /home/screener/env/screener.yml
RUN /home/screener/install/compile.sh

CMD ["/bin/bash"]


I get this error while running it into the docker file

#14 [8/8] RUN /home/screener/install/compile.sh

#14 0.246 fatal: could not create work tree dir 'Meeko': Permission denied

#14 0.246 /home/screener/install/compile.sh: line 9: cd: Meeko: No such file or directory

#14 0.247 fatal: not a git repository (or any of the parent directories): .git

#14 0.544 Defaulting to user installation because normal site-packages is not writeable

#14 0.808 ERROR: Directory '.' is not installable. Neither 'setup.py' nor 'pyproject.toml' found.

#14 0.866 Cloning into 'scrubber'...

#14 2.230 Defaulting to user installation because normal site-packages is not writeable

#14 2.275 Processing /home/scrubber

#14 2.277 Installing build dependencies: started

#14 3.353 Installing build dependencies: finished with status 'done'

#14 3.354 Getting requirements to build wheel: started

#14 3.660 Getting requirements to build wheel: finished with status 'done'

#14 3.661 Preparing metadata (pyproject.toml): started

#14 3.860 Preparing metadata (pyproject.toml): finished with status 'done'

#14 3.863 Requirement already satisfied: rdkit>=2022.03.1 in /opt/conda/envs/Screener/lib/python3.12/site-packages (from molscrub==0.1.1) (2025.3.5)

#14 3.864 Building wheels for collected packages: molscrub

#14 3.865 Building wheel for molscrub (pyproject.toml): started

#14 4.113 Building wheel for molscrub (pyproject.toml): finished with status 'done'

#14 4.114 Created wheel for molscrub: filename=molscrub-0.1.1-py3-none-any.whl size=62740 sha256=68204259f3e28cadb62b3bbcd27ad6be088ee7c675900b3d25e67069e0559628

#14 4.114 Stored in directory: /tmp/pip-ephem-wheel-cache-1k4h4pde/wheels/b5/a0/7e/f876af6b556ae4e28baf7845bbfdac9b0f9ff9a04e96710778

#14 4.117 Successfully built molscrub

#14 4.191 Installing collected packages: molscrub

#14 4.223 Successfully installed molscrub-0.1.1

#14 DONE 4.3s


compile.sh

#rdkit six from meeko
git clone https://github.com/forlilab/Meeko.git
cd Meeko
git checkout develop
micromamba run -n Screener pip install . --use-pep517 .
cd ..
rm -rf Meeko

#install scrubber
git clone https://github.com/forlilab/scrubber.git
cd scrubber
micromamba run -n Screener pip install --use-pep517 .
cd ..
rm -rf scrubber

Continue reading...