Added new Docker file for motif search (named meme-5.5.4) installed from...

Added new Docker file for motif search (named meme-5.5.4) installed from source, with all the necessary changes to use the new container for motif search. Updated the command line arguments for meme-chip to use v5.x syntax.

building/docker/chipseq/Dockerfile

+FROM continuumio/miniconda3:24.3.0-0
+
+LABEL IMAGE="chipseq" \
+    IMAGE_VERSION="1.0.0" \
+    AUTHORS="Felix Perez,Peng Lian" \
+    EMAIL="biohpc-help@utsouthwestern.edu"
+
+WORKDIR /chipseq/
+
+# Environment variables for the campus proxy.
+ENV http_proxy="http://proxy.swmed.edu:3128" \
+    https_proxy="http://proxy.swmed.edu:3128"
+
+    # Enable the use of bash-specific conda commands in the layer.
+RUN eval "$(conda shell.bash hook)" && \
+    # Create a Python 3.6.1 conda environment and initialize its use.
+    conda create -y -c bioconda -c defaults -c conda-forge -n py361 python=3.6.1 && \
+    echo "python ==3.6.1" >> /opt/conda/envs/py361/conda-meta/pinned && \
+    conda update conda -y && \
+    conda activate py361 && \
+    # Install the versions of numpy and pandas required for further software installs.
+    pip install numpy==1.12.1 && \
+    pip install pandas==0.20.1 && \
+    # Install BWA 0.7.12
+    conda install -y --solver=libmamba -c bioconda bwa=0.7.12 && \
+    # Install depedencies for the following installations.
+    apt-get update && apt-get install -y gcc make zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev && \
+    # Install Sambamba 0.6.6
+    conda install -y -c bioconda sambamba=0.6.6 && \
+    sambamba --version && \
+    # Install BEDTools 2.26.0
+    conda install -y -c bioconda bedtools=2.26.0 && \
+    bedtools --version && \
+    # Install Pandoc 2.7
+    conda install -y -c conda-forge pandoc=2.7 && \
+    pandoc --version && \
+    # Install deepTools 2.5.0.1
+    pip install deepTools==2.5.0.1 && \
+    deeptools --version && \
+    pip cache purge && \
+    conda deactivate && \
+    conda clean -y --all && \
+    apt-get remove -y gcc make zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev && \
+    apt-get clean
+
+RUN eval "$(conda shell.bash hook)" && \
+    # Install MultiQC v.1.9 & SAMtools 1.6 in a separate conda environment - unsatisfiable in py361.
+    conda create -y --solver=libmamba -c defaults -c conda-forge -c bioconda -n extra python=3.7.6 multiqc=1.9 samtools=1.6 && \
+    ln -s /opt/conda/envs/extra/bin/multiqc /usr/bin/multiqc && \
+    ln -s /opt/conda/envs/extra/bin/samtools /usr/bin/samtools && \
+    samtools --version && \
+    multiqc --version && \
+    conda deactivate && \
+    conda clean -y --all
+
+    # Create a Python 2.7 environment.
+RUN eval "$(conda shell.bash hook)" && \
+    conda create -y -n py27 -c conda-forge python=2.7.12 pip=9.0.1 && \
+    conda activate py27  && \
+    apt-get update && apt-get install -y gcc make zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev && \
+    # Install Trim Galore 0.4.1.
+    conda install -y --solver=libmamba -c bioconda trim-galore=0.4.1 && \
+    trim_galore --version && \
+    # Fix the version of cutadapt for trim galore.
+    conda install -y --solver=libmamba -c bioconda cutadapt=1.9.1 && \
+    cutadapt --version && \
+    # Install MACS2 2.1.0.20151222
+    pip install numpy && \
+    pip install MACS2==2.1.0.20151222 && \
+    macs2 --version && \
+    # Install phantompeakqualtools 1.2
+    conda install -y --solver=libmamba -c conda-forge gcc && \
+    conda install -y --solver=libmamba -c bioconda phantompeakqualtools=1.2 && \
+    # Install MEME 4.11.1
+    conda install -y --solver=libmamba -c bioconda meme=4.11.1 && \
+    meme -version && \
+    conda deactivate && \
+    conda clean -y --all && \
+    apt-get remove -y gcc make zlib1g-dev && \
+    apt-get remove -y libbz2-dev liblzma-dev libcurl4-openssl-dev && \
+    apt-get clean
+
+RUN eval "$(conda shell.bash hook)" && \
+    conda activate py27 && \
+    # Install R 3.4.1 & r-spp 1.14.
+    conda install -y --solver=libmamba -c conda-forge libiconv && \
+    conda install -y --solver=libmamba -c conda-forge r=3.4.1 && \
+    conda install -y --solver=libmamba -c bioconda r-spp=1.14 && \
+    conda deactivate && \
+    conda clean -y --all && \
+    # Setup the symlinks for the software in the py27 environment so that when 
+    # the Python 3.6.1 environment is active, users can still use commands
+    # that are dependent upon Python 2.7.
+    ln -s /opt/conda/envs/py27/bin/trim_galore /usr/bin/trim_galore && \
+    ln -s /opt/conda/envs/py27/bin/cutadapt /usr/bin/cutadapt && \
+    ln -s /opt/conda/envs/py27/bin/R /usr/bin/R && \
+    ln -s /opt/conda/envs/py27/bin/Rscript /usr/bin/Rscript && \
+    ln -s /opt/conda/envs/py27/bin/run_spp.R /usr/bin/run_spp.R && \
+    ln -s /opt/conda/envs/py27/bin/macs2 /usr/bin/macs2 && \
+    ln -s /opt/conda/envs/py27/bin/meme /usr/bin/meme && \
+    ln -s /opt/conda/envs/py27/bin/meme-chip /usr/bin/meme-chip
+
+# Install UCSC_userApps/v317
+RUN apt-get install -y gcc-9 g++-9 make libncurses-dev zlib1g-dev libbz2-dev liblzma-dev libcap-dev libssl-dev libpng-dev libmariadb-dev-compat libcurl4-openssl-dev && \
+    ln -fs /usr/bin/gcc-9 /usr/bin/gcc && \
+    wget http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v317.src.tgz && \
+    tar -xzf userApps.v317.src.tgz && \
+    rm userApps.v317.src.tgz && \
+    cd userApps && \
+    make clean && \
+    make && \
+    # In entrypoint.sh, an export command is used to add the userApps binaries to the PATH environment variable.
+    apt-get remove -y gcc-9 g++-9 make libncurses-dev zlib1g-dev libbz2-dev liblzma-dev libpcap-dev libssl-dev libpng-dev libmariadb-dev-compat libcurl4-openssl-dev && \
+    apt-get clean
+
+# Copy in the entrypoint script to use for activating the Python 3.6.1 conda environment by default when launching a container.
+COPY entrypoint.sh .
+
+RUN chmod +x entrypoint.sh
+
+ENTRYPOINT ["/chipseq/entrypoint.sh"]
\ No newline at end of file