Fix Docker image

.latest-version

@@ -1 +1 @@
-20230823010232
+20230823013659

Dockerfile

@@ -15,26 +15,27 @@ COPY hivfacts /sierra/hivfacts
 COPY src /sierra/src
 RUN /sierra/gradlew assemble
 RUN mv build/libs/sierra-*.war build/libs/sierra.war 2>/dev/null
-ENV MINIMAP2_VERSION=2.17
+ENV MINIMAP2_VERSION=2.26
+RUN apt-get -q update && apt-get install -qqy curl bzip2
 RUN cd /tmp && \
-    curl -sSL https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2 -o minimap2.tar.bz2 && \
+    curl -sSL https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2 -o minimap2.tar.bz2 && \
     tar jxf minimap2.tar.bz2 && \
     mv minimap2-${MINIMAP2_VERSION}_x64-linux /usr/local/minimap2
 
 FROM hivdb/tomcat-with-nucamino:latest as postalign-builder
-RUN apt-get -q update && apt-get install -qqy python3.9-full python3.9-dev gcc
+RUN apt-get -q update && apt-get install -qqy python3.11-full python3.11-dev gcc
 ADD https://bootstrap.pypa.io/get-pip.py /tmp/get-pip.py
-RUN python3.9 /tmp/get-pip.py
-RUN pip install cython==0.29.32
-ARG POSTALIGN_VERSION=3f99cc81ad89d66adf3beb062c93962f0deb3352
+RUN python3.11 /tmp/get-pip.py
+RUN pip install cython==0.29.35
+ARG POSTALIGN_VERSION=889295116cd5ac590e3929064551af82ee6741b4
 RUN pip install https://github.com/hivdb/post-align/archive/${POSTALIGN_VERSION}.zip
 
 FROM hivdb/tomcat-with-nucamino:latest
 ENV CATALINA_OPTS "-Xms1024M -Xmx6144M"
-RUN apt-get -q update && apt-get install -qqy python3.9
+RUN apt-get -q update && apt-get install -qqy python3.11
 COPY --from=builder /usr/local/minimap2 /usr/local/minimap2
 COPY --from=builder /sierra/build/libs/sierra.war /usr/share/tomcat/webapps
-COPY --from=postalign-builder /usr/local/lib/python3.9 /usr/local/lib/python3.9
+COPY --from=postalign-builder /usr/local/lib/python3.11 /usr/local/lib/python3.11
 COPY --from=postalign-builder /usr/local/bin/postalign /usr/local/bin/postalign
 RUN sed -i 's/<Context>/<Context privileged="true">/' /usr/share/tomcat/conf/context.xml
 RUN cd /usr/local/bin && \

docker/tomcat-with-nucamino/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 ENV LC_ALL=C.UTF-8
 ENV LANG=C.UTF-8
 ENV CATALINA_OPTS "-Xms512M -Xmx1024M"
@@ -9,7 +9,7 @@ RUN apt-get update -qy && \
     echo debconf shared/accepted-oracle-license-v1-3 select true | debconf-set-selections && \
     echo debconf shared/accepted-oracle-license-v1-3 seen true | debconf-set-selections && \
     apt-get install -qqy oracle-java17-installer oracle-java17-set-default
-ARG TOMCAT_VERSION=10.0.14
+ARG TOMCAT_VERSION=10.1.12
 RUN cd /tmp && \
     curl -sSL https://www.apache.org/dist/tomcat/tomcat-10/v${TOMCAT_VERSION}/bin/apache-tomcat-${TOMCAT_VERSION}.tar.gz -o tomcat10.tar.gz && \
     tar zxf tomcat10.tar.gz && \
@@ -22,10 +22,10 @@ RUN cd /tmp && \
     cp /usr/share/tomcat/conf/web.xml /root/web.prod.xml && \
     cp /root/web.prod.xml /usr/share/tomcat/conf/web.xml && \
     rm -rf /tmp/*
-ENV NUCAMINO_VERSION=0.2.0-beta.2
+# ENV NUCAMINO_VERSION=0.2.0-beta.2
 # RUN curl -L https://github.com/hivdb/NucAmino/releases/download/${NUCAMINO_VERSION}/nucamino-linux-amd64 -o /usr/bin/nucamino
-ADD nucamino-linux-amd64 /usr/bin/nucamino
+# ADD nucamino-linux-amd64 /usr/bin/nucamino
 EXPOSE 8080
 ADD src/hivdb-tomcat-entrypoint.sh /usr/bin/entrypoint
-RUN chmod +x /usr/bin/entrypoint /usr/bin/nucamino
+# RUN chmod +x /usr/bin/entrypoint /usr/bin/nucamino
 ENTRYPOINT ["/usr/bin/entrypoint"]

docker/tomcat-with-nucamino/Makefile

@@ -1,5 +1,5 @@
 build:
-	@docker pull ubuntu:18.04
+	@docker pull ubuntu:22.04
 	@docker build -t hivdb/tomcat-with-nucamino:latest .
 
 force-build: