INFRA-541 Combine main methods for Docker

hartwigmedical · Sep 6, 2024 · 26f4032 · 26f4032
1 parent b7db00a
commit 26f4032
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Showing 3 changed files with 18 additions and 2 deletions.
diff --git a/cuppa/Dockerfile b/cuppa/Dockerfile
@@ -8,4 +8,4 @@ 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 
 RUN pip3 install --upgrade pip && pip3 install /opt/tools/pycuppa
 
-ENTRYPOINT ["java", "-cp", "/usr/share/hartwig/cuppa.jar", "com.hartwig.hmftools.cup.prep.CuppaDataPrep"]
+ENTRYPOINT ["java", "-jar", "/usr/share/hartwig/cuppa.jar"]
diff --git a/cuppa/pom.xml b/cuppa/pom.xml
@@ -81,7 +81,7 @@
                     <archive>
                         <manifest>
                             <addClasspath>true</addClasspath>
-                            <mainClass>com.hartwig.hmftools.cup.CupAnalyser
+                            <mainClass>com.hartwig.hmftools.cup.cli.PrepPlusPredictionMain
                             </mainClass>
                             <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                             <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>

diff --git a/cuppa/src/main/java/com/hartwig/hmftools/cup/cli/PrepPlusPredictionMain.java b/cuppa/src/main/java/com/hartwig/hmftools/cup/cli/PrepPlusPredictionMain.java
@@ -0,0 +1,16 @@
+package com.hartwig.hmftools.cup.cli;
+
+import com.hartwig.hmftools.cup.prep.CuppaDataPrep;
+
+public class PrepPlusPredictionMain {
+    public static void main(String[] args) {
+        try {
+            CuppaDataPrep.main(args);
+            PredictionRunner.main(args);
+            System.exit(0);
+        } catch (Exception e) {
+            e.printStackTrace();
+            System.exit(1);
+        }
+    }
+}