bioconda install

[Noczio]

creating an image from a dockerfile based on rocker/shiny:4.0.5 and using RUN conda install -y -c bioconda svim never ends the installation. conda was installed this way:

# download Miniconda and install it
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda && \
rm Miniconda3-latest-Linux-x86_64.sh

# change default shell to bash
SHELL ["/bin/bash", "--login", "-c"]

# update PATH to include conda
ENV PATH /root/miniconda/bin:$PATH

# init conda bash, then create an env and finally activate it
RUN conda init bash && \
conda create -n appenv python=3.9 && \
echo "conda activate appenv" >> ~/.bashrc

# update conda and add bioconda channels
RUN conda update conda && \
conda config --add channels defaults && \
conda config --add channels bioconda && \
conda config --add channels conda-forge

I tried installing minimap2 and samtools with bioconda channel before and after svim. This issue might be something with old dependencies.

It works installing it from pip tho 🤔: RUN conda install -y pip && pip install -U wheel && pip install -U svim