wangjien/mosdepth-extended repository overview

FROM zlskidmore/mosdepth:latest

RUN apt-get update && apt-get install -y
samtools
python3
python3-pip
python3-dev
python3-venv
libz-dev
&& rm -rf /var/lib/apt/lists/*

RUN python3 -m venv /opt/venv &&
/opt/venv/bin/pip install --no-cache-dir
pysam
numpy
pandas &&
ln -s /opt/venv/bin/python /usr/local/bin/python &&
ln -s /opt/venv/bin/pip /usr/local/bin/pip RUN /opt/venv/bin/python -c "import subprocess, sys, os, tempfile, gzip, pysam, numpy, pandas; print('All libraries imported successfully')"

WORKDIR /data

CMD ["/opt/venv/bin/python", "-c", "import mosdepth; print('mosdepth and dependencies ready')"]