Initial commit

.gitignore

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+*.pyc
+*~

Dockerfile

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+# StructMAn docker container
+
+# Using Ubuntu 18.04 as the base image
+FROM ubuntu:18.04
+
+# Meta-data
+LABEL maintainer="Alexander Gress ([email protected])" \
+      description="A docker container for the Structural Mutation Annotation (StructMAn) software which provides \
+          the annotation of non-synonymous single-nucleotide polymorphisms (nsSNPs) in the \
+          context of the structural neighbourhood of the resulting amino acid variations in \
+          the protein. Its rationale is that if a mutation is located on an interaction \
+          interface between the protein and another protein, DNA, RNA or a small molecule, \
+          it is likely to interfere with this interaction."
+
+# Install and update the required dependencies for StructMAn
+RUN apt-get update \
+&& DEBIAN_FRONTEND=noninteractive apt-get install -y mysql-server \
+wget \
+curl \
+vim \
+less \
+gcc \
+gzip \
+python3.7 \
+python3.7-dev \
+python3.7-distutils \
+libboost-all-dev \
+libzeep-dev \
+libbz2-dev \
+libz-dev \
+autoconf \
+automake \
+autotools-dev \
+rsync \
+openbabel \
+ncbi-blast+ \
+python-mysqldb \
+mysql-client && \
+rm -rf /var/lib/apt/lists/* && \
+rm -rf /var/lib/mysql
+
+# Register the python version 3.7 in alternatives
+RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.7 1
+
+# Set python 3.7 as the default python3
+RUN update-alternatives --set python3 /usr/bin/python3.7
+
+# Upgrade pip to the latest version
+RUN curl -s https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
+python3 get-pip.py --force-reinstall && \
+rm get-pip.py
+
+# Install StructMAn Python dependencies
+RUN pip3 install numpy biopython matplotlib multiprocess pymysql python-igraph pickle5>=0.0.10 psutil
+RUN pip3 install https://s3-us-west-2.amazonaws.com/ray-wheels/latest/ray-1.1.0.dev0-cp37-cp37m-manylinux1_x86_64.whl
+
+# Install and setup MMseqs2
+RUN wget -O /opt/mmseqs-linux-sse41.tar.gz https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz; tar xvfz /opt/mmseqs-linux-sse41.tar.gz -C /opt/; ln -s /opt/mmseqs/bin/mmseqs /usr/local/bin/
+
+# Install xssp-3.0.7-mkdssp
+RUN wget -O /opt/xssp-3.0.7.tar.gz https://github.com/cmbi/hssp/releases/download/3.0.7/xssp-3.0.7.tar.gz; tar xvzf /opt/xssp-3.0.7.tar.gz -C /opt/; rm /opt/xssp-3.0.7.tar.gz
+RUN (cd /opt/xssp-3.0.7/; ./autogen.sh; ./configure; make mkdssp; make install)
+
+# Add the StructMAn source
+ADD ./structman_source /usr/structman_library/sources/
+
+# Copy the entrypoint script to implement all the configuration
+COPY docker-entrypoint.sh /usr/local/bin/
+RUN chmod +x /usr/local/bin/docker-entrypoint.sh
+
+# Default volumes to organize all the files under one roof and to allow backup
+VOLUME ["/structman/input_data/", "/structman/results/", "/structman/resources/", "/var/log/mysql/", "/var/lib/mysql/"]
+
+# Ports
+EXPOSE 3306/tcp
+
+# Initialization and setup
+ENTRYPOINT ["/usr/local/bin/docker-entrypoint.sh"]
+
+CMD ["mysqld"]