Dockerfile

FROM alpine:3.8 as transator
ARG TRANSATOR_BRANCH
ENV TRANSATOR_BRANCH=${TRANSATOR_BRANCH:-develop}
RUN apk update && apk add openjdk8 maven wget && \
    mkdir -p /transator-java && \
    wget -q -O - https://github.com/MicrobiologyETHZ/transator-java/archive/$TRANSATOR_BRANCH.tar.gz | tar xzf - --strip-components=1 -C /transator-java && \
    mvn clean install -X -f /transator-java/pom.xml -DskipTests && \
    mvn clean package -X -f /transator-java/pom.xml -DskipTests

# Note: moving to jre11-slim means that debian sid is used, which installs HMMER 3.2 instead of 3.1, which breaks the structure
# generation part with a String being used in an 
FROM tomcat:9-jre8-slim
MAINTAINER Chris Field <fieldc@ethz.ch>

RUN mkdir -p /python-pks/PKSPredictor
RUN mkdir /java-runner
RUN mkdir /NRPSPredictor2

ARG TRANSATOR_CORE_BRANCH
ENV TRANSATOR_CORE_BRANCH=${TRANSATOR_CORE_BRANCH:-develop}

ARG CLADIFICATION_REV
ENV CLADIFICATION_REV=${CLADIFICATION_REV:-1df40c1088decdd68bd3ba244b116cb7b938a703}
 
COPY --from=transator /transator-java/PKSPredictorWeb/target/PKSPredictorWeb.war $CATALINA_HOME/webapps/trans-AT-PKS.war
COPY --from=transator /transator-java/PKSPredictorREST/target/PKSPredictorREST.war $CATALINA_HOME/webapps/trans-AT-PKS#rest.war
COPY --from=transator /transator-java/Common/target/Common-2.0.jar /java-runner/Common-2.0.jar
COPY --from=transator /transator-java/PKSPredictorRunner/target/PKSPredictorRunner-2.0.jar /java-runner/PKSPredictorRunner.jar

RUN apt-get update && apt-get install -y --no-install-recommends libc6-i386 hmmer=3.1b2+dfsg-5 emboss wget python-biopython unzip && \
    wget -q -O - https://github.com/pcm32/TransATor-core/archive/$TRANSATOR_CORE_BRANCH.tar.gz \
     | tar xzf - --strip-components=1 -C /python-pks/PKSPredictor && \
    wget -O NRPSPredictor2.zip http://www.ebi.ac.uk/~pmoreno/NRPSpredictor2_20111113.zip && unzip -d /NRPSPredictor2/ NRPSPredictor2.zip && \
    rm NRPSPredictor2.zip && \
    mkdir -p /tmp/transator-pielLab && wget -q -O - https://github.com/PielLab/transator/archive/$CLADIFICATION_REV.tar.gz \
     | tar xzf - --strip-components=1 -C /tmp/transator-pielLab  && \
    mv /tmp/transator-pielLab/cladification / && rm -rf /tmp/transator-pielLab && \
    apt-get purge -y wget unzip && \
    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN mkdir -p /tomcat/conf/Catalina/localhost
ADD tomcat-setup/PKSPredictorREST.xml /tomcat/conf/Catalina/localhost/PKSPredictorREST.xml
ADD tomcat-setup/PKSPredictorWeb.xml /tomcat/conf/Catalina/localhost/PKSPredictorWeb.xml
# 
# # we need to set the preferences automatically
RUN ["java", "-cp", "/java-runner/PKSPredictorRunner.jar:/java-runner/Common-2.0.jar", "exec.PreferenceSetter", "PythonPath:;HMMERPath:/usr/bin;FuzzProPath:/usr/bin;ScriptPath:/python-pks/PKSPredictor/src/;HMMERModelPath:/cladification/ks_hmmer_models/PKSAllPlusClades_ConsSignal100.hmm;UseCluster:;TmpPath:/tmp;HMMEROtherModelsPath:/cladification/other_domains/otherModels;NRPS2Path:/NRPSPredictor2;MonomerMolsPath:/cladification/pks_mol_files/;AminoAcidsMolsPath:/cladification/aa_mol_files/"]
RUN ["java","-cp","/java-runner/Common-2.0.jar","encrypt.Encrypter","alph4num3r1c"]

# ENV CATALINA_OPTS=-verbose:class
# Expose port 80 to the host
EXPOSE 8080
#