feat: upgraded to version CryoSPARC 4.5.3.

.gitignore

+.secret/*
 *license_id*

Dockerfile.desktop

@@ -6,10 +6,10 @@ ENV DEBIAN_FRONTEND noninteractive
 COPY mozilla.pin /etc/apt/preferences.d/mozilla 
 RUN curl -fsSL https://www.mongodb.org/static/pgp/server-6.0.asc | gpg --dearmor -o /usr/share/keyrings/mongodb-6.0-keyring.gpg \
   && echo "deb [ arch=amd64,arch64 signed-by=/usr/share/keyrings/mongodb-6.0-keyring.gpg ] https://repo.mongodb.org/apt/ubuntu jammy/mongodb-org/6.0 multiverse" | tee /etc/apt/sources.list.d/mongodb-org-6.0.list \
-  && apt-get update \
+  && apt-get update -y \
   && wget -q https://packages.mozilla.org/apt/repo-signing-key.gpg -O /usr/share/keyrings/packages.mozilla.org.asc \
   && echo "deb [ arch=amd64 signed-by=/usr/share/keyrings/packages.mozilla.org.asc ] https://packages.mozilla.org/apt mozilla main" > /etc/apt/sources.list.d/mozilla.list \
-  && apt-get update \
+  && apt-get update -y \
   && apt-get install -y --no-install-recommends \
     firefox \
     zip unzip \
@@ -76,8 +76,9 @@ RUN ${CRYOSPARC_MASTER_DIR}/deps/anaconda/envs/cryosparc_master_env/bin/python3
 ARG MOTIONCOR2_VERSION=1.4.5
 ENV MOTIONCOR2_VERSION=${MOTIONCOR2_VERSION}
 ENV CUDA_TOOLKIT_VERSION="Cuda100-10-22-2021"
-RUN cd /usr/local/bin \
-  && curl -L 'https://drive.google.com/uc?export=download&id=1-Ub5lBBmel8U8U0uibORiH6wfxp9I1kn' > MotionCor2_${MOTIONCOR2_VERSION}.zip \
+RUN --mount=type=secret,id=motioncor2_license_id \
+  && cd /usr/local/bin \
+  && curl -L 'https://drive.google.com/uc?export=download&id=$(cat /run/secrets/motioncor2_license_id)' > MotionCor2_${MOTIONCOR2_VERSION}.zip \
   && unzip MotionCor2_${MOTIONCOR2_VERSION}.zip \
   && rm -f MotionCor2_${MOTIONCOR2_VERSION}.zip \
   && ln -sf MotionCor2_${MOTIONCOR2_VERSION}-${CUDA_TOOLKIT_VERSION} MotionCor2
@@ -88,7 +89,9 @@ RUN cd /usr/local/bin \
 ARG TOPAZ_VERSION=0.2.5
 ENV TOPAZ_VERSION=${TOPAZ_VERSION}
 ENV TOPAZ_CUDA_TOOLKIT_VERSION=12.2.0
-RUN /app/cryosparc_worker/deps/anaconda/bin/conda install topaz=${TOPAZ_VERSION} cuda-libraries-dev cuda-nvcc cuda-nvtx cuda-cupti -c nvidia/label/cuda-${TOPAZ_CUDA_TOOLKIT_VERSION} -c tbepler -c pytorch
+RUN ${CRYOSPARC_WORKER_DIR}/deps/anaconda/bin/conda install topaz=${TOPAZ_VERSION} cuda-libraries-dev cuda-nvcc cuda-nvtx cuda-cupti -c nvidia/label/cuda-${TOPAZ_CUDA_TOOLKIT_VERSION} -c tbepler -c pytorch
+RUN ${CRYOSPARC_WORKER_DIR}/deps/anaconda/bin/conda create -n topaz python=3.6
+COPY topaz.sh ${CRYOSPARC_WORKER_DIR}/deps/anaconda/bin/topaz.sh
 
 ###
 #

Makefile

-CRYOSPARC_VERSION ?= 4.4.1
-CRYOSPARC_PATCH ?= 240110
-CRYOSPARC_RELEASE ?= 3
+CRYOSPARC_VERSION ?= 4.5.3
+CRYOSPARC_PATCH ?= 
+CRYOSPARC_RELEASE ?= 0
 
 CONTAINER_RUNTIME ?= docker
 IMAGE ?= slaclab/cryosparc-desktop
@@ -11,22 +11,29 @@ CRYOSPARC_FULL_VERSION = $(CRYOSPARC_VERSION)
 else
 CRYOSPARC_FULL_VERSION = $(CRYOSPARC_VERSION)+$(CRYOSPARC_PATCH)
 endif
+ifeq ($(CRYOSPARC_RELEASE),)
+TAG = $(subst +,-,$(CRYOSPARC_FULL_VERSION))
+else
 TAG = $(subst +,-,$(CRYOSPARC_FULL_VERSION)-$(CRYOSPARC_RELEASE))
+endif
 CRYOSPARC_IMAGE_INSTALL_DIR = /sdf/group/cryoem/sw/images/cryosparc/$(CRYOSPARC_FULL_VERSION)-desktop
 
 echo_tag: tag
 	echo "TAG=$(TAG)"
 
 license:
-	mkdir .secret
-	echo ${CRYOSPARC_LICENSE_ID} > .secret/license_id.txt
+	mkdir -p etc/.secrets
+	echo ${CRYOSPARC_LICENSE_ID} > etc/.secrets/cryosparc_license_id.txt
+        echo ${MOTIONCOR2_LICENSE_ID} > etc/.secrets/motioncor2_license_id.txt
 
 build: tag
 	COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 $(CONTAINER_RUNTIME) build \
 		--build-arg CRYOSPARC_VERSION=${CRYOSPARC_VERSION} \
 		--build-arg CRYOSPARC_PATCH=${CRYOSPARC_PATCH} \
+		--platform linux/amd64 \
 		--progress=plain \
-		--secret id=cryosparc_license_id,src=.secret/license_id.txt \
+		--secret id=cryosparc_license_id,src=etc/.secrets/cryosparc_license_id.txt \
+		--secret id=motioncor2_license_id,src=etc/.secrets/motioncor2_license_id.txt \
 		. -f Dockerfile.desktop \
 	-t $(IMAGE):${TAG}
 

cryosparc.desktop

 [Desktop Entry]
 Type=Application
-Exec=sh ./cryosparc_launcher.sh
+Exec=bash cryosparc_launcher.sh
 Hidden=false
 X-GNOME-Autostart-enabled=true
 Name=CryoSPARC Web App

cryosparc.sh

@@ -54,12 +54,16 @@ THIS_USER=$(whoami)
 THIS_USER_SUFFIX=${USER_SUFFIX:-'slac.stanford.edu'}
 ACCOUNT="${THIS_USER}@${THIS_USER_SUFFIX}"
 rm -f "${SOCK_FILE}" || true
+cryosparcm start database
+cryosparcm fixdbport
 cryosparcm restart
 
 # ensure that the mongo replset is correct
 MONGO_PORT=$(( $CRYOSPARC_BASE_PORT + 1 ))
 export CRYOSPARC_MONGO_EXTRA_FLAGS="  --unixSocketPrefix ${LSCRATCH}"
+${CRYOSPARC_MASTER_DIR}/bin/cryosparcm start database
 ${CRYOSPARC_MASTER_DIR}/bin/cryosparcm fixdbport
+${CRYOSPARC_MASTER_DIR}/bin/cryosparcm restart
 
 # creat cryosparc local accounts
 create_account() {
@@ -78,6 +82,8 @@ if [ -e "/init.d/accounts" ]; then
 fi
 
 # need to restart to get login prompt
+cryosparcm start database
+cryosparcm fixdbport
 cryosparcm restart
 
 echo "Success starting cryosparc master!"

topaz.sh

+#!/bin/bash --login
+
+if command -v conda > /dev/null 2>&1; then
+    conda deactivate > /dev/null 2>&1 || true  # ignore any errors
+    conda deactivate > /dev/null 2>&1 || true  # ignore any errors
+fi
+unset _CE_CONDA
+unset CONDA_DEFAULT_ENV
+unset CONDA_EXE
+unset CONDA_PREFIX
+unset CONDA_PROMPT_MODIFIER
+unset CONDA_PYTHON_EXE
+unset CONDA_SHLVL
+unset PYTHONPATH
+unset LD_PRELOAD
+unset LD_LIBRARY_PATH
+
+set -euo pipefail
+set +euo pipefail
+export BIN_PATH=/app/cryosparc_worker/deps/anaconda/bin
+${BIN_PATH}/activate topaz_env
+set -euo pipefail
+
+exec ${BIN_PATH}/topaz $@