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FROM continuumio/miniconda3:24.3.0-0
LABEL IMAGE="chipseq-analysis-motifSearch" \
IMAGE_VERSION="1.0.0" \
AUTHORS="Felix Perez,Peng Lian" \
EMAIL="biohpc-help@utsouthwestern.edu"
WORKDIR /motif-search/
# Environment variables for the campus proxy.
ENV http_proxy="http://proxy.swmed.edu:3128" \
https_proxy="http://proxy.swmed.edu:3128"
# Original module load order:
# module load python/3.6.1-2-anaconda
# module load meme/4.11.1-gcc-openmpi
# module load bedtools/2.26.0
COPY entrypoint.sh .
RUN eval "$(conda shell.bash hook)" && \
conda create -y -c bioconda -c conda-forge -c defaults -n motifSearch python=2.7.12 pip=9.0.1 && \
echo "python ==2.7.12" >> /opt/conda/envs/motifSearch/conda-meta/pinned && \
conda activate motifSearch && \
# Install pandas and numpy.
pip install numpy==1.12.1 && \
pip install pandas==0.20.1 && \
# Install MEME 4.11.1
conda install -y --solver=libmamba -c conda-forge -c bioconda meme=4.11.1 && \
meme -version && \
# Install BEDTools 2.26.0
conda install -y --solver=libmamba -c bioconda bedtools=2.26.0 && \
bedtools --version && \
# The stringi installation below solves a dependency issue encountered when DREME is used (meme-4.11.1)
conda install -y --solver=libmamba -c conda-forge r-stringi=1.2.4 && \
conda deactivate
RUN eval "$(conda shell.bash hook)" && \
# Create a Python 3.6.1 conda environment and initialize its use.
conda create -y -c bioconda -c defaults -c conda-forge -n py361 python=3.6.1 && \
echo "python ==3.6.1" >> /opt/conda/envs/py361/conda-meta/pinned && \
conda update conda -y && \
conda activate py361 && \
# Install the versions of numpy and pandas required for further software installs.
pip install numpy==1.12.1 && \
pip install pandas==0.20.1 && \
conda deactivate && \
ln -s /opt/conda/envs/py361/bin/python3 /opt/conda/envs/motifSearch/bin/python3
RUN chmod +x entrypoint.sh
ENTRYPOINT ["/motif-search/entrypoint.sh"]