Changed the install lanes scripts so that users can update lanes created by HPCE

scripts/configure_cryosparc_for_slurm.sh

@@ -1,41 +0,0 @@
-#!/bin/bash
-
-# Check that CRYOSPARC_HOME is set and directory exists
-if [ -z "$CRYOSPARC_HOME" ]; then
-    echo "Error: CRYOSPARC_HOME is not set."
-    return 1
-fi
-
-if [ ! -d "$CRYOSPARC_HOME" ]; then
-    echo "Error: CRYOSPARC_HOME directory '$CRYOSPARC_HOME' does not exist."
-    return 1
-fi
-
-cd "$CRYOSPARC_HOME" || { echo "Failed to change directory to $CRYOSPARC_HOME"; return 1; }
-
-echo "Cloning merlin7 branch of merlin-cryosparc into 'config' directory..."
-if git clone -b merlin7 git@gitea.psi.ch:CLS-IT/merlin-cryosparc.git config; then
-    echo "Clone successful."
-else
-    echo "Git clone failed."
-    return 1
-fi
-
-# Define remote host
-remote_host="merlin7-cryosparc01.psi.ch"
-
-echo "Running install_filter on remote host..."
-if ssh "$USER@$remote_host" install_filter; then
-    echo "install_filter command completed successfully."
-else
-    echo "install_filter command failed."
-    return 1
-fi
-
-echo "Running connect_all on remote host..."
-if ssh "$USER@$remote_host" connect_all; then
-    echo "connect_all command completed successfully."
-else
-    echo "connect_all command failed."
-    return 1
-fi

scripts/install_cryosparc_lanes.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+
+# Set CryoSPARC installation directory
+CRYOSPARC_HOME="/data/user/$USER/cryosparc"
+
+# Check that CRYOSPARC_HOME is set and directory exists
+if [ -z "$CRYOSPARC_HOME" ]; then
+    echo "Error: CRYOSPARC_HOME is not set."
+    return 1
+fi
+
+if [ ! -d "$CRYOSPARC_HOME" ]; then
+    echo "Error: CRYOSPARC_HOME directory '$CRYOSPARC_HOME' does not exist."
+    return 1
+fi
+
+cd "$CRYOSPARC_HOME" || { echo "Failed to change directory to $CRYOSPARC_HOME"; return 1; }
+
+# Check if 'config' directory already exists
+if [ -d "config/.git" ]; then
+    echo "'config' directory already exists. Attempting to pull latest changes..."
+    cd config || { echo "Failed to change directory to config"; return 1; }
+
+    # Check if we're on the correct branch
+    current_branch=$(git rev-parse --abbrev-ref HEAD)
+    if [ "$current_branch" != "merlin7" ]; then
+        echo "Switching to 'merlin7' branch..."
+        git fetch origin merlin7 && git checkout merlin7 || { echo "Failed to switch to merlin7 branch"; return 1; }
+    fi
+
+    git pull || { echo "Git pull failed."; return 1; }
+    echo "Repository updated successfully."
+else
+    echo "Cloning merlin7 branch of merlin-cryosparc into 'config' directory..."
+    if git clone -b merlin7 git@gitea.psi.ch:CLS-IT/merlin-cryosparc.git config; then
+        echo "Clone successful."
+    else
+        echo "Git clone failed."
+        return 1
+    fi
+fi
+
+# Define remote host
+remote_host="merlin7-cryosparc01.psi.ch"
+
+echo "Running install_filter on remote host..."
+if ssh "$USER@$remote_host" install_filter; then
+    echo "install_filter command completed successfully."
+else
+    echo "install_filter command failed."
+    return 1
+fi
+
+echo "Running connect_all on remote host..."
+if ssh "$USER@$remote_host" connect_all; then
+    echo "connect_all command completed successfully."
+else
+    echo "connect_all command failed."
+    return 1
+fi

scripts/install_cryosparc_worker.sh

@@ -1,5 +1,8 @@
 #!/bin/bash
 
+# Set CryoSPARC installation directory
+CRYOSPARC_HOME="/data/user/$USER/cryosparc"
+
 # Check CRYOSPARC_HOME
 if [ -z "$CRYOSPARC_HOME" ]; then
     echo "Error: CRYOSPARC_HOME is not set."