Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git

.github/workflows/dockerbuild.yml

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+name: Build and push docker images
+
+on:
+  push:
+    branches: [master]
+
+jobs:
+  build-and-push:
+    name: Build image and push to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      name: Checkout source code
+    - name: Build the Docker image
+      run: |
+        tag="ibiosim:snapshot"
+        echo $tag
+        docker build . --tag $tag
+    - uses: azure/docker-login@v1
+      with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+    - name: Push the image to Docker Hub
+      run: |
+        tag="ibiosim:snapshot"
+        echo $tag
+        docker push $tag

Dependencies/newbuild.sh

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+#!/bin/bash
+
+BUILD_DIR=$PWD
+ROOT=/iBioSim
+
+tar -xf libSBML-5.15.2-core-plus-packages-src.tar.gz
+tar -xf gsl-latest.tar.gz
+tar -xf GeneNet.tar.gz
+tar -xf reb2sac.tar.gz
+
+# Install gsl
+cd ${BUILD_DIR}/gsl-2.4
+./configure --prefix=${ROOT} --quiet
+make --quiet
+make install --quiet
+
+# Install libsbml
+cd ${BUILD_DIR}/libSBML-5.15.2-Source
+./configure --prefix=${ROOT} --with-java --enable-comp --quiet
+make --quiet; make --quiet
+make install --quiet
+
+# Install GeneNet
+cd ${BUILD_DIR}/GeneNet
+make --quiet
+cp bin/GeneNet ${ROOT}/bin/GeneNet.linux64
+cp ${ROOT}/bin/GeneNet.linux64 ${ROOT}/bin/GeneNet
+
+
+# Install reb2sac
+cd ${BUILD_DIR}/reb2sac
+CFLAGS="-I${ROOT}/include -O0 -g3 -DNAME_FOR_ID" LDFLAGS="-L${ROOT}/lib -lm" ./configure --prefix=${ROOT}/ && \
+    env WANT_AUTOCONF_2_5="1" WANT_AUTOMAKE_1_6="1" make -k -j1 install
+cp ${ROOT}/bin/reb2sac ${ROOT}/bin/reb2sac.linux64

Dockerfile

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+FROM ubuntu:18.04
+
+LABEL base_image="ubuntu:18.04"
+LABEL version="1.0.0"
+LABEL software="bioSimAPI"
+LABEL software.version="1.0.0"
+LABEL about.summary="API for SynBioHub/SBOLCanvas communication with iBioSim"
+LABEL about.home="https://github.com/MyersResearchGroup/iBioSim"
+LABEL about.documentation="https://github.com/MyersResearchGroup/iBioSim"
+LABEL about.license_file="https://github.com/MyersResearchGroup/iBioSim/blob/master/LICENSE.txt"
+LABEL about.license="Apache-2.0"
+LABEL about.tags="kinetic modeling,dynamical simulation,systems biology,biochemical networks,SBML,SED-ML,COMBINE,OMEX,BioSimulators"
+LABEL maintainer="Chris Myers <chris.myers@colorado.edu>"
+
+# Install requirements
+RUN apt-get update --fix-missing \
+	&& DEBIAN_FRONTEND=noninteractive \
+	&& apt-get install -y maven \
+	&& apt-get install python3.7 -y \
+	&& apt-get install python3-pip -y \
+	&& apt install openjdk-8-jdk -y 
+
+# Build iBioSim
+WORKDIR /iBioSim
+COPY . .
+RUN mvn package -Dmaven.javadoc.skip=true
+WORKDIR /
+
+RUN apt-get -y install build-essential \
+	&& apt-get -y install dos2unix \
+	&& apt-get -y install libxml2-dev
+
+# Build reb2sac
+WORKDIR iBioSim/Dependencies
+RUN chmod +x newbuild.sh \
+	&& dos2unix newbuild.sh \
+	&& sh newbuild.sh
+WORKDIR /
+
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8