Fixing bug with BEAST2

JBris · Dec 31, 2024 · 856f54e · 856f54e
1 parent 0973ab9
commit 856f54e
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Showing 3 changed files with 11 additions and 16 deletions.
diff --git a/Apptainer.v2.7.3 b/Apptainer.v2.7.3
@@ -8,4 +8,4 @@ From: ghcr.io/jbris/beast2:v2.7.3
     This is an image to run BEAST2.
 
 %runscript
-    exec beast -packagedir /usr/local/lib "$@"
+    exec /usr/local/beast/bin/beast "$@"
diff --git a/Dockerfile.v2.7.3 b/Dockerfile.v2.7.3
@@ -4,7 +4,7 @@ ARG APP_VERSION
 
 ARG DEBIAN_FRONTEND=noninteractive
 
-WORKDIR /usr
+WORKDIR /usr/local
 
 COPY workspace /usr/local/workspace
 
@@ -15,31 +15,26 @@ RUN apt-get update \
     && curl -fsSLO https://github.com/CompEvol/beast2/releases/download/${APP_VERSION}/BEAST.${APP_VERSION}.Linux.x86.tgz \
     && tar fxz BEAST.${APP_VERSION}.Linux.x86.tgz \
     && rm BEAST.${APP_VERSION}.Linux.x86.tgz \
-    && mv beast/bin/* /usr/local/bin \
-    && mv beast/lib/* /usr/local/lib \
-    && mv beast/jre /usr/local \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* \
     && rm -rf /tmp/downloaded_packages \
-    && packagemanager -dir /usr/local/lib -add BADTRIP \
-    && packagemanager -dir /usr/local/lib -add PoMo \
-    && packagemanager -dir /usr/local/lib -add phylodynamics 
+    && /usr/local/beast/bin/packagemanager -add BADTRIP \
+    && /usr/local/beast/bin/packagemanager -add PoMo \
+    && /usr/local/beast/bin/packagemanager -add PhyDyn 
+# && packagemanager -dir /usr/local/lib -add phylodynamics \
 # && packagemanager -dir /usr/local/lib -add BEAST_CLASSIC \ 
 # && packagemanager -dir /usr/local/lib -add Babel \ 
 # && packagemanager -dir /usr/local/lib -add MultiTypeTree \
-# && packagemanager -dir /usr/local/lib -add PhyDyn \
 # && packagemanager -dir /usr/local/lib -add Recombination \
-# && packagemanager -dir /usr/local/lib -add ReMASTER
+# && packagemanager -dir /usr/local/lib -add ReMASTER \
 
-ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+ENV LD_LIBRARY_PATH=/usr/local/beast/lib:$LD_LIBRARY_PATH
 
-RUN chmod -R +x /usr/local/bin \
-    && chmod -R +x /usr/local/jre \
-    && chmod -R +rwx /usr/local/lib \
+RUN chmod -R +x /usr/local \
     && chmod -R +rwx /usr/local/workspace
 
 WORKDIR /usr/local/workspace
 
 EXPOSE 5900
 
-CMD [ "beast", "-packagedir", "/usr/local/lib"]
+CMD [ "/usr/local/beast/bin/beast"]
diff --git a/workspace/scripts/run.sh b/workspace/scripts/run.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
 
 cd ..
-docker compose run --rm beast2 beast -packagedir /usr/local/lib $@
+docker compose run --rm beast2 /usr/local/beast/bin/beast $@
 cd workspace