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Merge pull request #7 from ajshedivy/cytoscape
Cytoscape
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‎.github/workflows/test.yml‎

Lines changed: 34 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -20,31 +20,14 @@ jobs:
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auto-activate-base: false
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auto-update-conda: false
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miniconda-version: 'latest'
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# Log conda environment contents
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- name: Log conda environment
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shell: bash --login {0}
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run: conda list
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# Run the PCSF tests in the pcsf conda environment
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- name: Test PCSF
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shell: bash --login {0}
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run: pytest pcsf/tests/
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workflow:
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name: Test TPS workflow
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest]
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Install conda environment
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uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: tps_workflow
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environment-file: workflow/minimal_env.yml
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auto-activate-base: false
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miniconda-version: 'latest'
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# Run the workflow tests
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- name: Test workflow
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shell: bash --login {0}
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# Verbose output and disable stdout and stderr capturing
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run: pytest -vs workflow/tests/
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docker:
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name: Build Docker images
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runs-on: ${{ matrix.os }}
@@ -58,7 +41,7 @@ jobs:
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uses: docker/build-push-action@v1
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with:
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path: .
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dockerfile: docker/tps/Dockerfile
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dockerfile: containers/tps/Dockerfile
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repository: ajshedivy/tps
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tags: latest
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cache_froms: ajshedivy/tps:latest
@@ -67,8 +50,36 @@ jobs:
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uses: docker/build-push-action@v1
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with:
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path: .
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dockerfile: docker/cytoscape/Dockerfile
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dockerfile: containers/cytoscape/Dockerfile
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repository: ajshedivy/cytoscape
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tags: latest
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cache_froms: ajshedivy/cytoscape:latest
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push: false
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workflow:
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name: Test TPS workflow
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest]
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Install conda environment
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uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: tps_workflow
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environment-file: workflow/minimal_env.yml
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auto-activate-base: false
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miniconda-version: 'latest'
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# Log conda environment contents
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- name: Log conda environment
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shell: bash --login {0}
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run: conda list
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# Run the workflow tests
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- name: Test workflow with pytest
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shell: bash --login {0}
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# Verbose output and disable stdout and stderr capturing
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run: pytest -vs workflow/tests/
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- name: Test workflow with script
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shell: bash --login {0}
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run: bash workflow.sh --config workflow/config/default_config.yaml --execute all

‎containers/__init__.py‎

Whitespace-only changes.

docker/cytoscape/Dockerfile renamed to containers/cytoscape/Dockerfile

Lines changed: 42 additions & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -1,42 +1,42 @@
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# The following docker image is derived from a containerized version
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# of Cytoscape with GUI support
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#
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# https://github.com/cytoscape/docker-cytoscape-desktop
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FROM ubuntu:20.04
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# PARAMETERS
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ENV CYTOSCAPE_VERSION=3.8.2
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# CHANGE USER
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USER root
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# https://github.com/cytoscape/cytoscape/releases/download/3.8.2/cytoscape-unix-3.8.2.tar.gz
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# INSTALL JAVA
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RUN apt-get update && apt-get -y install default-jdk libxcursor1 xvfb supervisor wget x11vnc
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RUN wget https://github.com/cytoscape/cytoscape/releases/download/${CYTOSCAPE_VERSION}/cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz
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RUN tar xf cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz && rm cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz
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# Set JAVA_HOME From sudo update-alternatives --config java
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RUN echo 'JAVA_HOME="/usr/lib/jvm/java-11-openjdk-amd64"' >> /etc/environment
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ENV JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
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ENV PATH /opt/conda/bin:$PATH
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RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh -O ~/miniconda.sh && \
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/bin/bash ~/miniconda.sh -b -p /opt/conda && \
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rm ~/miniconda.sh && \
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/opt/conda/bin/conda clean --all && \
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ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
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echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
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conda init bash
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COPY docker/cytoscape/env.yml /docker/minimal_env.yml
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RUN conda env create -f docker/minimal_env.yml
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COPY docker/cytoscape/supervisor/supervisord.conf /etc/supervisor/conf.d/supervisord.conf
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COPY docker/cytoscape/src/connect_cytoscape.py /cytoscape/connect_cytoscape.py
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COPY docker/cytoscape/src/connect.sh /cytoscape/connect.sh
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EXPOSE 1234 5900
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CMD ["/usr/bin/supervisord > /dev/null 2>&1"]
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# The following docker image is derived from a containerized version
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# of Cytoscape with GUI support
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#
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# https://github.com/cytoscape/docker-cytoscape-desktop
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6+
FROM ubuntu:20.04
7+
8+
# PARAMETERS
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ENV CYTOSCAPE_VERSION=3.8.2
10+
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# CHANGE USER
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USER root
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# https://github.com/cytoscape/cytoscape/releases/download/3.8.2/cytoscape-unix-3.8.2.tar.gz
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# INSTALL JAVA
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RUN apt-get update && apt-get -y install default-jdk libxcursor1 xvfb supervisor wget x11vnc
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RUN wget https://github.com/cytoscape/cytoscape/releases/download/${CYTOSCAPE_VERSION}/cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz
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RUN tar xf cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz && rm cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz
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# Set JAVA_HOME From sudo update-alternatives --config java
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RUN echo 'JAVA_HOME="/usr/lib/jvm/java-11-openjdk-amd64"' >> /etc/environment
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ENV JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
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ENV PATH /opt/conda/bin:$PATH
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RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh -O ~/miniconda.sh && \
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/bin/bash ~/miniconda.sh -b -p /opt/conda && \
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rm ~/miniconda.sh && \
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/opt/conda/bin/conda clean --all && \
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ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
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echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
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conda init bash
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34+
COPY containers/cytoscape/env.yml /docker/minimal_env.yml
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RUN conda env create -f /docker/minimal_env.yml
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COPY containers/cytoscape/supervisor/supervisord.conf /etc/supervisor/conf.d/supervisord.conf
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COPY containers/cytoscape/src/connect_cytoscape.py /cytoscape/connect_cytoscape.py
39+
COPY containers/cytoscape/src/connect.sh /cytoscape/connect.sh
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EXPOSE 1234 5900
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CMD ["/usr/bin/supervisord > /dev/null 2>&1"]

‎containers/cytoscape/__init__.py‎

Whitespace-only changes.

docker/cytoscape/env.yml renamed to containers/cytoscape/env.yml

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
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name: tps_workflow
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channels:
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- conda-forge
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- defaults
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dependencies:
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- python=3.6
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- pip=20.0
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- pip:
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name: tps_workflow
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channels:
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- conda-forge
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- defaults
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dependencies:
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- python=3.6
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- pip=20.0
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- pip:
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- py2cytoscape==0.7.1

‎containers/cytoscape/src/__init__.py‎

Whitespace-only changes.

‎containers/cytoscape/src/connect.sh‎

Lines changed: 71 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,71 @@
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#!/bin/bash
2+
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if (($# == 0)); then
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exit 0
5+
fi
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POSITIONAL_ARGS=()
8+
9+
while [[ $# -gt 0 ]]; do
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case $1 in
11+
-s|--save)
12+
SAVE="$2"
13+
shift # past argument
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shift # past value
15+
;;
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-y|--style)
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STYLE="$2"
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shift # past argument
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shift # past value
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;;
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-a|--annot)
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ANNOTATIONS="$2"
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shift # past argument
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shift # past value
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;;
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-n|--network)
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NETWORK="$2"
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shift # past argument
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shift # past value
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;;
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-d|--datatypes)
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DATATYPES="$2"
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shift # past argument
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shift # past value
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;;
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-*|--*)
37+
echo "Unknown option $1"
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exit 1
39+
;;
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*)
41+
POSITIONAL_ARGS+=("$1") # save positional arg
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shift # past argument
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;;
44+
esac
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done
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set -- "${POSITIONAL_ARGS[@]}" # restore positional parameters
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48+
echo "SAVE FILE = ${SAVE}"
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echo "STYLE FILE = ${STYLE}"
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echo "ANNOTATIONS FILE = ${ANNOTATIONS}"
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echo "NETWORK FILE = ${NETWORK}"
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echo "DATA TYPES = ${DATATYPES}"
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54+
if [[ -n $1 ]]; then
55+
echo "error: invalid arguments"
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exit 0
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fi
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echo "activate TPS environment"
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eval "$(conda shell.bash hook)"
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conda activate tps_workflow
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63+
if [ $? -ne 0 ]; then
64+
echo "environment does not exist"
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echo "creating TPS environment"
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conda env create -f /docker/minimal_env.yml
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conda activate tps_workflow
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fi
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echo "environment activated"
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python connect_cytoscape.py --save ${SAVE} --style ${STYLE} --annot ${ANNOTATIONS} --network ${NETWORK} --datatypes ${DATATYPES}

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