.gitignore

@@ -103,9 +103,18 @@ ENV/
 
 # nextflow analysis folders/files
 pipeline_trace*.txt*
+dag.dot*
 .nextflow*.log*
 report*.html*
 timeline*.html*
-/workflow/output/*
-/work/*
-/.nextflow/*
+test_data/*.fastq.gz
+workflow/dag*.dot*
+workflow/trace*.txt*
+workflow/.nextflow/
+workflow/.nextflow*.log*
+workflow/report*.html*
+workflow/timeline*.html*
+workflow/output/*
+workflow/work/*
+workflow/images/
+workflow/cleanup.sh

astrocyte_pkg.yml

@@ -9,15 +9,31 @@
 # A unique identifier for the workflow package, text/underscores only
 name: 'chipseq_analysis_bicf'
 # Who wrote this?
-author: 'Holly Ruess, Spencer D. Barnes, Jeremy A. Mathews, Beibei Chen and Venkat Malladi'
+author: 'Holly Ruess, Spencer D. Barnes, Jeremy A. Mathews, Beibei Chen and Venkat Malladi, Peng Lian, Felix Perez'
 # A contact email address for questions
 email: 'bicf@utsouthwestern.edu'
 # A more informative title for the workflow package
 title: 'BICF ChIP-seq Analysis Workflow'
 # A summary of the workflow package in plain text
 description: |
-  This is a workflow package for the BioHPC/BICF ChIP-seq workflow system.
-  It implements ChIP-seq analysis workflow and visualization application.
+  This is a fully-containerized version of the workflow package for the
+  BioHPC/BICF ChIP-seq workflow system. It implements the ChIP-seq analysis
+  workflow and visualization application.
+
+# The minimum Astrocyte version that requires to run this workflow. For old pipelines, which do not have this label
+# a default value of 0.3.1 will be assigned automatically. A request of minimum version less than 0.4.0 will be ignored.
+minimum_astrocyte_version: '2.0.1'
+# The Nextflow version that requires to run this workflow.  For old pipelines, which do not have this label
+# a default value of 0.31.0 will be assigned automatically. Please make sure the requested nextflow version is available
+# in the module list.
+nextflow_version: '19.07.0'
+
+# (Optional) The Nextflow config file to use for this workflow. If provided, the file should exist in workflow/configs
+nextflow_config: 'biohpc.config'
+# The container to use for this workflow, none/singularity. If omitted, the default value 'none' will be used.
+container: 'singularity'
+# The version of singularity to use. This is required if container == 'singularity'
+singularity_version: '3.9.9'
 
 # -----------------------------------------------------------------------------
 # DOCUMENTATION
@@ -39,21 +55,20 @@ documentation_files:
 # A list of cluster environment modules that this workflow requires to run.
 # Specify versioned module names to ensure reproducability.
 workflow_modules:
-  - 'python/3.6.1-2-anaconda'
-  - 'trimgalore/0.4.1'
-  - 'bwa/intel/0.7.12'
-  - 'samtools/1.6'
-  - 'sambamba/0.6.6'
-  - 'bedtools/2.26.0'
-  - 'deeptools/2.5.0.1'
-  - 'phantompeakqualtools/1.2'
-  - 'macs/2.1.0-20151222'
-  - 'UCSC_userApps/v317'
-  - 'R/3.3.2-gccmkl'
-  - 'meme/4.11.1-gcc-openmpi'
-  - 'pandoc/2.7'
-  - 'singularity/3.0.2'
-
+  - None
+
+# A list of container images requires to run this workflow.
+# Specify full path and version names to ensure reproducibility.
+# This keyword is required when 'container' is specified in Astrocyte 0.4.1 and above.
+# Singularity supports different registries, please specify the protocol to use.
+# Such as, "docker://", "shub://", "library://", etc. We encourage you to use the GitLab
+# container registry of BioHPC to save and manage your container images.
+workflow_containers:
+  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/py36:1.0.0
+  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/r:3.3.2
+  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/python:3.6.1
+  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0
+  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/motif-search:meme-5.5.4
 
 # A list of parameters used by the workflow, defining how to present them,
 # options etc in the web interface. For each parameter:

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

building/docker/chipseq/entrypoint.sh

+#!/bin/bash --login
+# The --login ensures the bash configuration is loaded, enabling Conda.
+
+# Temporarily disable strict mode and activate conda:
+# set : Used to set or unset shell attributes (when options are specified, as shown here).
+# -e : Exit on non-zero return status.
+# -u : Treat unset variables and parameters other than special parameters "@" and "*" as an error when performaing parameter expansion.
+# -o : specify an option name. In our case here, we use the "pipefail" option.
+# pipefail : If set, the return value of a pipeline is the value of the last (rightmost) command to exit with a non-zeros status, or zero if all commands in the pipeline exit successfully.
+# Using + rather than - causes these options to be turned off.
+set +euo pipefail
+
+source /opt/conda/etc/profile.d/conda.sh
+
+conda activate py361
+
+# Add the userApps binaries to the PATH.
+export PATH=$PATH:/chipseq/userApps/bin/
+
+# Enable strict mode:
+set -euo pipefail
+
+# exec some commands:
+exec "$@"

building/docker/motif-search/meme-4.11.1/Dockerfile

+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"]

building/docker/motif-search/meme-4.11.1/entrypoint.sh

+#!/bin/bash --login
+# The --login ensures the bash configuration is loaded, enabling Conda.
+
+# Temporarily disable strict mode and activate conda:
+# set : Used to set or unset shell attributes (when options are specified, as shown here).
+# -e : Exit on non-zero return status.
+# -u : Treat unset variables and parameters other than special parameters "@" and "*" as an error when performaing parameter expansion.
+# -o : specify an option name. In our case here, we use the "pipefail" option.
+# pipefail : If set, the return value of a pipeline is the value of the last (rightmost) command to exit with a non-zeros status, or zero if all commands in the pipeline exit successfully.
+# Using + rather than - causes these options to be turned off.
+set +euo pipefail
+
+source /opt/conda/etc/profile.d/conda.sh
+
+conda activate motifSearch
+
+export PATH=/motif-search/meme/bin/:$PATH
+
+# Enable strict mode:
+set -euo pipefail
+
+# exec the final command:
+exec "$@"

building/docker/motif-search/meme-5.5.4/Dockerfile

+#FROM ubuntu:20.04
+FROM continuumio/miniconda3:24.3.0-0
+
+WORKDIR /motif-search/
+
+ENV DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC
+
+# Environment variables for the campus proxy.
+ENV http_proxy="http://proxy.swmed.edu:3128" \
+    https_proxy="http://proxy.swmed.edu:3128"
+
+COPY ./meme-5.5.4.tar.gz  .
+# RUN wget https://meme-suite.org/meme/meme-software/5.5.4/meme-5.5.4.tar.gz
+RUN tar -zxf ./meme-5.5.4.tar.gz 
+RUN rm meme-5.5.4.tar.gz 
+
+COPY entrypoint.sh . 
+
+RUN apt update \
+    && apt-get install -y --no-install-recommends \
+    wget \
+	build-essential \
+    ca-certificates \
+    curl \
+    imagemagick \
+    libexpat1-dev \
+    libxml2-dev \
+	libxslt1-dev \
+	libgs-dev \
+    libgd-dev \
+	#libexslt1-dev \
+    python3 \
+    zlib1g-dev \
+	perl \
+	libxml-simple-perl \
+	libxml-libxml-perl \
+	libxml-parser-perl \
+	libhtml-template-compiled-perl \
+    libxml-opml-simplegen-perl \
+    libxml-libxml-debugging-perl \
+    && apt-get clean 
+  
+# Install meme-chip
+RUN cd meme-5.5.4 && \
+    ./configure --prefix=/motif-search/meme --with-url="http://meme-suite.org" --enable-build-libxml2 --enable-build-libxslt && \
+    make && \
+    # make test && \
+    make install && \
+	export PATH=/motif-search/meme/bin/:/motif-search/meme/libexec/meme-5.5.4:$PATH && \
+    meme -version && \
+    meme-chip --version && \
+    spamo --version && \
+    centrimo --version && \
+    # apt-get remove -y build-essential libxml2 libxml2-dev libxslt1-dev && \
+    apt-get clean
+
+# Enable the use of bash-specific conda commands in the layer.
+RUN eval "$(conda shell.bash hook)" && \
+    chmod +x entrypoint.sh && \
+    #conda create -y -c bioconda -c conda-forge -c defaults -n motifSearch python=2.7.12 pip=9.0.1 && \
+    conda create -y -c bioconda -c conda-forge -c defaults -n motifSearch python=3.6.1 && \
+	conda activate motifSearch && \
+    python --version && \
+    # Install pandas and numpy.
+    pip install numpy==1.12.1 && \
+    pip install pandas==0.20.1 && \
+    # Install BEDTools 2.26 .0
+    conda install -y --solver=libmamba -c bioconda bedtools=2.26.0 && \
+    bedtools --version && \
+    conda clean -y --all && \
+    conda deactivate 
+
+ENTRYPOINT ["/motif-search/entrypoint.sh"]

building/docker/motif-search/meme-5.5.4/entrypoint.sh

+#!/bin/bash --login
+# The --login ensures the bash configuration is loaded, enabling Conda.
+
+# Temporarily disable strict mode and activate conda:
+# set : Used to set or unset shell attributes (when options are specified, as shown here).
+# -e : Exit on non-zero return status.
+# -u : Treat unset variables and parameters other than special parameters "@" and "*" as an error when performaing parameter expansion.
+# -o : specify an option name. In our case here, we use the "pipefail" option.
+# pipefail : If set, the return value of a pipeline is the value of the last (rightmost) command to exit with a non-zeros status, or zero if all commands in the pipeline exit successfully.
+# Using + rather than - causes these options to be turned off.
+set +euo pipefail
+
+source /opt/conda/etc/profile.d/conda.sh
+
+conda activate motifSearch
+
+export PATH=/motif-search/meme/bin/:$PATH
+
+# Enable strict mode:
+set -euo pipefail
+
+# exec the final command:
+exec "$@"

building/docker/podman.py

+#!/usr/bin/python3
+
+import sys
+import json
+import subprocess
+import threading
+
+'''
+This script is a wrapper of the podman command on RHEL 7. It helps podman 1.6.4 to push a correct manifest file the
+remote registry.
+
+Author: Peng Lian
+Date: 10/24/2023
+'''
+
+
+PODMAN_BIN = subprocess.check_output(['which', 'podman']).decode().strip()
+
+def execute_command(command, *args):
+    '''
+    Execute command and print the real time output to stdout
+    '''
+
+    # Function to process and print output in real time
+    def process_output(pipe):
+        for line in pipe:
+            print(line.decode(), end="")
+
+    cmd = [command, *args]
+    with subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) as process:
+        stdout_thread = threading.Thread(target=process_output, args=(process.stdout,))
+        stderr_thread = threading.Thread(target=process_output, args=(process.stderr,))
+
+        stdout_thread.start()
+        stderr_thread.start()
+
+        # Wait for the process to complete
+        process.wait()
+
+        # Ensure that both threads finish
+        stdout_thread.join()
+        stderr_thread.join()
+
+        return process.returncode
+
+
+def fix_manifest(registry, tag):
+    '''
+    '.gzip' is missing in the 'mediaType' of 'layers' in the manifest file generated by podman 1.6.4.
+    This function scans the 'mediaType' and add the '.gzip' suffix.
+    '''
+    print(f'Fixing manifest for {registry}:{tag} ...')
+
+    # get graph root
+    output = subprocess.check_output([PODMAN_BIN, 'info', '-f', 'json'])
+    info = json.loads(output.decode())
+    graphRoot = info['store']['GraphRoot']
+
+    # get image ID
+    output = subprocess.check_output([PODMAN_BIN, 'inspect', f'{registry}:{tag}'])
+    imageID = eval(output.decode().replace('true', 'True').replace('false', 'False'))[0]['Id']
+
+    # read manifest
+    imageManifestFile = f'{graphRoot}/overlay-images/{imageID}/manifest'
+    manifest = json.loads(open(imageManifestFile).readlines()[0])
+
+    # update the layers mediaType with .gzip
+    changed = False
+    for l in manifest['layers']:
+        if l['mediaType'].endswith('tar'):
+            l['mediaType'] = f"{l['mediaType']}.gzip"
+            changed = True
+
+    # write the fixed manifest to file
+    if changed:
+        with open(imageManifestFile, 'w') as f:
+            f.write(json.dumps(manifest).replace(' ', '') + '\n')
+        f.close()
+        print('Manifest updated.')
+
+    return json.dumps(manifest)
+
+
+if __name__ == "__main__":
+
+    # only engage when 'push' command is called
+    if len(sys.argv) >= 2 and sys.argv[1] == 'push':
+        print(f"Executing push: {' '.join(sys.argv[1:])}")
+
+        # get registry and tag from the last argv
+        last_argv = sys.argv[-1]
+        if last_argv.find(':') > 0:
+            Tag = last_argv.strip().split(':')[-1]
+            Registry = ':'.join(last_argv.strip().split(':')[:-1])
+
+            # fix manifest
+            fix_manifest(registry=Registry, tag=Tag)
+
+        execute_command(PODMAN_BIN, *sys.argv[1:])
+    else:
+        execute_command(PODMAN_BIN, *sys.argv[1:])

building/docker/python-3.6.1/Dockerfile

+FROM continuumio/miniconda3:24.3.0-0
+
+LABEL IMAGE="Python/3.6.1" \
+    IMAGE_VERSION="0.0.1" \
+    AUTHORS="Felix Perez,Peng Lian" \
+    EMAIL="biohpc-help@utsouthwestern.edu"
+
+WORKDIR /python361/
+
+# Environment variables for the campus proxy.
+ENV http_proxy="http://proxy.swmed.edu:3128" \
+    https_proxy="http://proxy.swmed.edu:3128"
+
+# Copy in files to use for activating our Python 3.6.1 conda environment by default when launching a container.
+COPY entrypoint.sh .
+
+RUN chmod +x entrypoint.sh && \
+    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 && \
+    # Enable the use of bash-specific conda commands in the layer.
+    eval "$(conda shell.bash hook)" && \
+    conda update conda -y && \
+    conda activate py361 && \
+    # Install pandas and numpy
+    pip install numpy==1.12.1 && \
+    pip install pandas==0.20.1 && \
+    conda clean -y --all && \
+    pip cache purge && \
+    conda deactivate
+
+#ENV BASH_ENV="/python361/entrypoint.sh"
+RUN chmod +x entrypoint.sh
+ENTRYPOINT ["/python361/entrypoint.sh"]
+CMD ["/opt/conda/envs/py361/bin/python"]
+

building/docker/python-3.6.1/Dockerfile_non_conda

+FROM ubuntu:18.04
+
+LABEL IMAGE="Python/3.6.1" \
+    IMAGE_VERSION="0.0.1" \
+    AUTHORS="Felix Perez,Peng Lian" \
+    EMAIL="biohpc-help@utsouthwestern.edu"
+
+WORKDIR /python361/
+
+# Environment variables for the campus proxy.
+ENV http_proxy="http://proxy.swmed.edu:3128" \
+    https_proxy="http://proxy.swmed.edu:3128"
+
+
+
+RUN apt-get update
+RUN apt-get install -y build-essential
+
+# This will install Python, pip, pip3, and pip3.6.
+RUN apt-get install -y python3.6-venv
+RUN apt-get install -y python3-pip
+
+# Inorder to run pip3.6, run it the following way `python3.6 -m pip`
+# Update Python & Install wheel
+RUN python3.6 -m pip install pip --upgrade
+RUN python3.6 -m pip install wheel
+RUN python3.6 -m pip install numpy==1.12.1
+RUN python3.6 -m pip install pandas==0.20.1 

building/docker/python-3.6.1/entrypoint.sh

+#!/bin/bash --login
+# The --login ensures the bash configuration is loaded, enabling Conda.
+
+# Temporarily disable strict mode and activate conda:
+# set : Used to set or unset shell attributes (when options are specified, as shown here).
+# -e : Exit on non-zero return status.
+# -u : Treat unset variables and parameters other than special parameters "@" and "*" as an error when performaing parameter expansion.
+# -o : specify an option name. In our case here, we use the "pipefail" option.
+# pipefail : If set, the return value of a pipeline is the value of the last (rightmost) command to exit with a non-zeros status, or zero if all commands in the pipeline exit successfully.
+# Using + rather than - causes these options to be turned off.
+set +euo pipefail
+
+source /opt/conda/etc/profile.d/conda.sh
+
+conda activate py361
+
+# Enable strict mode:
+set -euo pipefail
+
+# exec the final command:
+exec "$@"

building/docker/r-3.3.2/Dockerfile

+FROM continuumio/miniconda3:24.3.0-0
+
+LABEL IMAGE="R-3.3.2" \
+    IMAGE_VERSION="1.0.0" \
+    AUTHORS="Felix Perez,Peng Lian" \
+    EMAIL="biohpc-help@utsouthwestern.edu"
+
+WORKDIR /r-332/
+
+# Environment variables for the campus proxy.
+ENV http_proxy="http://proxy.swmed.edu:3128" \
+    https_proxy="http://proxy.swmed.edu:3128"
+
+RUN conda create -y -c bioconda -c defaults -c conda-forge -n r332 r-base=3.3.2 && \
+    echo "r-base ==3.3.2" >> /opt/conda/envs/r332/conda-meta/pinned && \
+    # Enable the use of bash-specific conda commands in the layer.
+    eval "$(conda shell.bash hook)" && \
+    conda update conda -y && \
+    conda activate r332 && \
+    # Install ChIPseeker, GenomicFeatures, and DiffBind from Bioconductor
+    conda install -y --solver=libmamba -c bioconda bioconductor-chipseeker=1.10.0 && \
+    conda install -y --solver=libmamba -c bioconda bioconductor-genomicfeatures=1.26.4 && \
+    conda install -y --solver=libmamba -c bioconda bioconductor-diffbind=2.2.12 && \
+    # The below install solves a dependency issue with libicui18n.so
+    conda install -y --solver=libmamba -c conda-forge r-stringi && \
+    R -e "as.data.frame(installed.packages()[,c(1,3:4)])" && \
+    conda clean -y --all && \
+    conda deactivate
+
+# Copy in the entrypoint.sh script used to activate the R 3.3.2 conda environment by default when launching a container.
+COPY entrypoint.sh .
+
+RUN chmod +x entrypoint.sh
+
+ENTRYPOINT ["/r-332/entrypoint.sh"]
+CMD ["/opt/conda/envs/r-332/bin/R"]
+

building/docker/r-3.3.2/Rprofile.site

+options(repos = c(CRAN = 'https://cloud.r-project.org'), download.file.method = 'libcurl')
+options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')
+options(Ncpus = 6)
+

building/docker/r-3.3.2/entrypoint.sh

+#!/bin/bash --login
+# The --login ensures the bash configuration is loaded, enabling Conda.
+
+# Temporarily disable strict mode and activate conda:
+# set : Used to set or unset shell attributes (when options are specified, as shown here).
+# -e : Exit on non-zero return status.
+# -u : Treat unset variables and parameters other than special parameters "@" and "*" as an error when performaing parameter expansion.
+# -o : specify an option name. In our case here, we use the "pipefail" option.
+# pipefail : If set, the return value of a pipeline is the value of the last (rightmost) command to exit with a non-zeros status, or zero if all commands in the pipeline exit successfully.
+# Using + rather than - causes these options to be turned off.
+set +euo pipefail
+
+source /opt/conda/etc/profile.d/conda.sh
+
+conda activate r332
+
+# Enable strict mode:
+set -euo pipefail
+
+# exec the final command:
+exec "$@"