removed hardcoded plugins

Dockerfile

@@ -25,22 +25,26 @@ RUN echo "" | /opt/scipion/scipion config
 RUN sed -i 's/MPI_LIBDIR\s*=.*/MPI_LIBDIR = \/usr\/lib\/x86_64-linux-gnu\/openmpi\/lib/' /opt/scipion/config/scipion.conf && \
     sed -i 's/MPI_INCLUDE\s*=.*/MPI_INCLUDE = \/usr\/lib\/x86_64-linux-gnu\/openmpi\/include/' /opt/scipion/config/scipion.conf
 
-COPY plugin-list-pl.txt /plugin-list-pl.txt
-COPY plugin-list-bin.txt plugin-list-bin.txt
+COPY plugin-list-pl.txt /
+COPY plugin-list-bin.txt /
 
 RUN export CORE_COUNT=$(nproc) && \
     /opt/scipion/scipion install -j $CORE_COUNT && \
     \
-    for pl in $(cat plugin-list-pl.txt); do /opt/scipion/scipion installp -p $pl -j $CORE_COUNT; done && \
+    for pl in $(cat /plugin-list-pl.txt); do /opt/scipion/scipion installp -p $pl -j $CORE_COUNT; done && \
     \
-    for bin in $(cat plugin-list-bin.txt); do /opt/scipion/scipion installb $bin -j $CORE_COUNT; done
+    for bin in $(cat /plugin-list-bin.txt); do /opt/scipion/scipion installb $bin -j $CORE_COUNT; done
 
-#RUN tar -czf /scipion-docker-plugin-volume.tar.gz /opt/scipion/software/em
+RUN cd /opt/scipion/software/ && for file in $(ls -A); do if [ "$file" != "em" ]; then rm -rf $file; fi; done
+RUN cd /opt/scipion/ && for file in $(ls -A); do if [ "$file" != "software" ]; then rm -rf $file; fi; done
+RUN cd /opt/ && for file in $(ls -A); do if [ "$file" != "scipion" ]; then rm -rf $file; fi; done
 
-#RUN rm /opt/scipion/software/em/*.tgz
+RUN ls -la /opt
+RUN ls -la /opt/scipion
+RUN ls -la /opt/scipion/software/em
 
-RUN mv /opt/scipion/software/em /scipion-plugin-volume
-RUN rm -rf /opt/scipion
+RUN mv /plugin-list-pl.txt /opt/scipion/software/em/ && \
+    mv /plugin-list-bin.txt /opt/scipion/software/em/
 
 COPY docker-entrypoint.sh /docker-entrypoint.sh
 RUN chmod +x /docker-entrypoint.sh

docker-entrypoint.sh

@@ -2,4 +2,5 @@
 
 set -x
 
-cp -r /scipion-plugin-volume/* /volume/
+cp -r /opt/scipion/software/em/* /volume/
+