Hardcode a few bits for this particular esvee version

Author: brainstorm

.github/workflows/release.yml

@@ -36,12 +36,22 @@ jobs:
         registry: ghcr.io
         username: ${{ github.actor }}
         password: ${{ secrets.GITHUB_TOKEN }}
+#    - name: Get git tag tool and version
+#      run: |
+#        TAG=${GITHUB_REF#refs/tags/}
+#        TOOL=${TAG%-*}
+#        VERSION=${TAG#*-}
+#        echo "TOOL=$TOOL" >> $GITHUB_ENV
+#        echo "VERSION=$VERSION" >> $GITHUB_ENV
     - name: Docker GitHub release
       uses: docker/build-push-action@v6
       with:
         context: .
         provenance: false
         file: ./esvee/Dockerfile
         platforms: ${{ matrix.platforms }}
+#        build-args: VERSION=$VERSION
+        build-args: VERSION=1.0.2
         push: true
+#        tags: ghcr.io/umccr/hmftools-$TOOL:$VERSION-aarch64
         tags: ghcr.io/umccr/hmftools-esvee:1.0.2-aarch64

esvee/Dockerfile

@@ -8,7 +8,8 @@ ARG RUN_SCRIPT=/usr/local/bin/${TOOL_NAME}
 USER root
 
 ADD target/${TOOL_NAME}-${VERSION}-jar-with-dependencies.jar ${JAR}
-ADD entrypoint.sh ${RUN_SCRIPT}
+#ADD entrypoint.sh ${RUN_SCRIPT}
+ADD ./esvee/entrypoint.sh ${RUN_SCRIPT}
 RUN chmod +x ${RUN_SCRIPT}
 
 RUN micromamba install -y -n base -c bioconda -c conda-forge \

esvee/entrypoint.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+set -euo pipefail
+
+TOOL="esvee"
+VERSION="1.0.2"
+
+# Parse arguments
+jvm_mem_opts=""
+jvm_gen_opts=""
+declare -a app_args
+for arg in "$@"; do
+  case ${arg} in
+    '-Xm'*)
+      jvm_mem_opts="${jvm_mem_opts} ${arg}"
+      ;;
+    '-D'* | '-XX'*)
+      jvm_gen_opts="${jvm_gen_opts} ${arg}"
+      ;;
+    *)
+      app_args+=("${arg}")
+      ;;
+  esac
+done
+
+# Form and execute command
+if [[ ${app_args[0]:=} == com.hartwig.* ]]; then
+  java ${jvm_mem_opts} ${jvm_gen_opts} -cp /usr/share/java/${TOOL}_v${VERSION}.jar ${app_args[@]}
+else
+  java ${jvm_mem_opts} ${jvm_gen_opts} -jar /usr/share/java/${TOOL}_v${VERSION}.jar ${app_args[@]}
+fi
+