INFRA-541 Add R deps for Cuppa

hartwigmedical · Sep 10, 2024 · c4b1d26 · c4b1d26
1 parent 85aae64
commit c4b1d26
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diff --git a/cuppa/Dockerfile b/cuppa/Dockerfile
@@ -7,7 +7,7 @@ RUN curl https://europe-west4-apt.pkg.dev/doc/repo-signing-key.gpg | apt-key add
 RUN echo 'deb http://packages.cloud.google.com/apt apt-transport-artifact-registry-stable main' | tee -a /etc/apt/sources.list.d/artifact-registry.list
 RUN apt update && apt install -y apt-transport-artifact-registry
 RUN echo 'deb ar+https://europe-west4-apt.pkg.dev/projects/hmf-build hmf-apt main' | tee -a  /etc/apt/sources.list.d/artifact-registry.list
-RUN apt update && apt install -y hmf-r-base 
+RUN apt update && apt install -y hmf-r-base hmf-r-ggplot2 hmf-r-ggh4x hmf-r-stringr hmf-r-patchwork
 
 ADD target/cuppa-$VERSION-jar-with-dependencies.jar /usr/share/hartwig/cuppa.jar
 RUN cd /opt/tools && jar xvf /usr/share/hartwig/cuppa.jar pycuppa 

diff --git a/cuppa/src/main/java/com/hartwig/hmftools/cup/cli/ShellCommand.java b/cuppa/src/main/java/com/hartwig/hmftools/cup/cli/ShellCommand.java
@@ -81,6 +81,7 @@ public ShellCommand run()
                     .start();
 
             mComplete = process.waitFor(mTimeout, mTimeoutUnit);
+            CUP_LOGGER.info("Command [{}] complete", this);
             mStdout = captureStdout(process, mLogLevel);
             mExitCode = process.exitValue();
         }