Update dockerfile and recipe

Author: stephen-riggs

Dockerfiles/tomo_align

@@ -34,15 +34,16 @@ ENV PATH=/install/venv/bin:${PATH}
 ENV LD_LIBRARY_PATH=/install/venv/lib:${LD_LIBRARY_PATH}
 
 # Install IMOD
+RUN yum groupinstall "Development Tools" -y
+RUN yum install mesa-libGL -y
 RUN mkdir imod_install && \
     curl https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_5.1.9_RHEL8-64_CUDA12.0.sh > imod_5.1.9_RHEL8-64_CUDA12.0.sh && \
     chmod +x imod_5.1.9_RHEL8-64_CUDA12.0.sh && \
-    ln -s /install/venv/bin/python /usr/bin/python3 && \
     ./imod_5.1.9_RHEL8-64_CUDA12.0.sh -dir imod_install -skip -y
 ENV PATH=/imod_install/IMOD/bin:${PATH}
 ENV IMOD_DIR=/imod_install/IMOD
 
 # Install AreTomo
-COPY --chown="${userid}":"${groupid}" packages/AreTomo2 /AreTomo2
-ENV PATH=/AreTomo2:${PATH}
-RUN chmod +x /AreTomo2
+COPY --chown="${userid}":"${groupid}" packages/AreTomo3 /AreTomo3
+ENV PATH=/AreTomo3:${PATH}
+RUN chmod +x /AreTomo3

recipes/ispyb/sxt-imod-beads-wbp.json

@@ -31,7 +31,8 @@
       "stack_file": "{stack_file}",
       "tilt_axis": 0,
       "txrm_file": "{txrm_file}",
-      "wbp": 1
+      "wbp": 1,
+      "xrm_reference": "{xrm_reference}"
     },
     "queue": "tomo_align_imod",
     "service": "ImodTomoAlign"

recipes/ispyb/sxt-imod-patch-wbp.json

@@ -31,7 +31,8 @@
       "stack_file": "{stack_file}",
       "tilt_axis": 0,
       "txrm_file": "{txrm_file}",
-      "wbp": 1
+      "wbp": 1,
+      "xrm_reference": "{xrm_reference}"
     },
     "queue": "tomo_align_imod",
     "service": "ImodTomoAlign"