commit 714bd3bd3b54754254f4d8cbd6ab351eb6013847
Author: João Pedro Agostinho de Sousa <joao.agostinho-de-sousa@psi.ch>
Date:   Tue Jul 1 09:12:27 2025 +0200

    First commit

diff --git a/README.md b/README.md
new file mode 100644
index 0000000..bfed65e
--- /dev/null
+++ b/README.md
@@ -0,0 +1,6 @@
+# Installing CryoSPARC on Merlin 7
+
+This repository contains the necessary scripts to install CryoSPARC on the Merlin 7 cluster.
+
+For the complete installation guide, please refer to the following page:
+https://intranet.psi.ch/en/cls/cryosparc-merlin-7-installation
diff --git a/scripts/configure_cryosparc_for_slurm.sh b/scripts/configure_cryosparc_for_slurm.sh
new file mode 100755
index 0000000..bb584ee
--- /dev/null
+++ b/scripts/configure_cryosparc_for_slurm.sh
@@ -0,0 +1,41 @@
+#!/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@$remote_host" connect_all; then
+    echo "connect_all command completed successfully."
+else
+    echo "connect_all command failed."
+    return 1
+fi
diff --git a/scripts/create_cryosparc_user.sh b/scripts/create_cryosparc_user.sh
new file mode 100755
index 0000000..f4d59ac
--- /dev/null
+++ b/scripts/create_cryosparc_user.sh
@@ -0,0 +1,46 @@
+#!/bin/bash
+
+# Define remote host
+remote_host="merlin7-cryosparc01.psi.ch"
+
+echo "------------------------------------------------------------"
+echo "CryoSPARC User Creation Script"
+echo "This script will help you create a new CryoSPARC user on the"
+echo "remote master node ($remote_host)."
+echo "You will be prompted for the user's email, username, name,"
+echo "and password, and then asked to confirm before proceeding."
+echo "------------------------------------------------------------"
+echo
+
+# Prompt for inputs
+read -rp "Enter your first name: " cryo_firstname
+read -rp "Enter your last name: " cryo_lastname
+read -rp "Enter your PSI email: " cryo_user_email
+read -rp "Enter your CryoSPARC login username: " cryo_username
+read -rsp "Enter your CryoSPARC password: " cryo_user_password
+echo
+
+# Confirm user input
+read -rp "Do you wish to proceed with user creation? (y/n): " confirm
+
+if [[ "$confirm" != [Yy]* ]]; then
+    echo "Aborted."
+    return 1
+fi
+
+# Execute createuser command on remote host
+echo "Creating user on CryoSPARC at $remote_host..."
+ssh "$USER@$remote_host" "cryosparcm createuser \
+    --email '$cryo_user_email' \
+    --password '$cryo_user_password' \
+    --username '$cryo_username' \
+    --firstname '$cryo_firstname' \
+    --lastname '$cryo_lastname'"
+
+# Check if creation was successful
+if [ $? -eq 0 ]; then
+    echo "✅ User '$cryo_username' created successfully."
+else
+    echo "❌ Failed to create user."
+    return 1
+fi
diff --git a/scripts/install_cryosparc_master.sh b/scripts/install_cryosparc_master.sh
new file mode 100755
index 0000000..97f2b82
--- /dev/null
+++ b/scripts/install_cryosparc_master.sh
@@ -0,0 +1,82 @@
+#!/bin/bash
+
+# Set CryoSPARC installation directory
+CRYOSPARC_HOME="/data/user/$USER/cryosparc"
+
+# Check if CRYOSPARC_HOME already exists and is not empty
+if [ -d "$CRYOSPARC_HOME" ] && [ "$(ls -A "$CRYOSPARC_HOME")" ]; then
+    echo "Warning: CryoSPARC home directory already exists at: $CRYOSPARC_HOME"
+    read -rp "Are you sure you want to overwrite it? [y/N]: " confirm
+    case "$confirm" in
+        [yY][eE][sS]|[yY])
+            echo -e "\nProceeding with installation and overwriting existing directory."
+            ;;
+        *)
+            echo -e "\nInstallation aborted by user."
+            return 0
+            ;;
+    esac
+fi
+
+# Create CryoSPARC home directory
+mkdir -p "$CRYOSPARC_HOME"
+cd "$CRYOSPARC_HOME" || { echo "Failed to enter directory $CRYOSPARC_HOME"; return 1; }
+echo "CryoSPARC home directory ready at: $CRYOSPARC_HOME"
+
+# Set and create temporary directory
+export TMPDIR="/scratch/$USER"
+mkdir -p "$TMPDIR"
+
+# Prompt for license ID
+read -rp "Enter your CryoSPARC License ID: " CRYOSPARC_LICENSE_ID
+if [ -z "$CRYOSPARC_LICENSE_ID" ]; then
+    echo "Error: License ID is required."
+    return 1
+fi
+
+# Prompt for base port
+read -rp "Enter CryoSPARC base port: " CRYOSPARC_BASE_PORT
+if ! [[ "$CRYOSPARC_BASE_PORT" =~ ^[0-9]+$ ]]; then
+    echo "Error: Port must be a number."
+    return 1
+fi
+
+# Download and extract CryoSPARC master package
+echo "Downloading CryoSPARC master package..."
+curl -L -o cryosparc_master.tar.gz "https://get.cryosparc.com/download/master-latest/$CRYOSPARC_LICENSE_ID"
+if [ $? -ne 0 ]; then
+    echo "Download failed. Please check your license ID and internet connection."
+    return 1
+fi
+
+echo "Extracting CryoSPARC master package..."
+tar -xf cryosparc_master.tar.gz && rm cryosparc_master.tar.gz
+echo "CryoSPARC master package extracted."
+
+cd cryosparc_master || { echo "Failed to enter cryosparc_master directory"; return 1; }
+
+# Define remote host
+remote_host="merlin7-cryosparc01.psi.ch"
+
+# Run installer
+echo "Running CryoSPARC installer..."
+./install.sh --license "$CRYOSPARC_LICENSE_ID" \
+             --hostname "$remote_host" \
+             --dbpath "$CRYOSPARC_HOME/database" \
+             --port "$CRYOSPARC_BASE_PORT"
+
+# Start CryoSPARC master process
+INSTALL_EXIT_CODE=$?
+if [ $INSTALL_EXIT_CODE -eq 0 ]; then
+    echo "CryoSPARC installation completed successfully."
+
+    echo "Attempting to start CryoSPARC master process on $remote_host..."
+    ssh "$USER@$remote_host" "cryosparcm start"
+    if [ $? -eq 0 ]; then
+        echo "CryoSPARC master process started successfully on $remote_host."
+    else
+        echo "Failed to start CryoSPARC master process on $remote_host."
+    fi
+else
+    echo "CryoSPARC installation failed with exit code $INSTALL_EXIT_CODE. Not attempting to start master process."
+fi
diff --git a/scripts/install_cryosparc_worker.sh b/scripts/install_cryosparc_worker.sh
new file mode 100755
index 0000000..29d3b80
--- /dev/null
+++ b/scripts/install_cryosparc_worker.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+# Check CRYOSPARC_HOME
+if [ -z "$CRYOSPARC_HOME" ]; then
+    echo "Error: CRYOSPARC_HOME is not set."
+    return 1
+fi
+
+cd "$CRYOSPARC_HOME" || { echo "Failed to enter directory $CRYOSPARC_HOME"; return 1; }
+
+# Check license ID
+if [ -z "$CRYOSPARC_LICENSE_ID" ]; then
+    read -rp "Enter your CryoSPARC License ID: " CRYOSPARC_LICENSE_ID
+    if [ -z "$CRYOSPARC_LICENSE_ID" ]; then
+        echo "Error: License ID is required."
+        return 1
+    fi
+fi
+
+echo "Downloading CryoSPARC worker package..."
+curl -L -o cryosparc_worker.tar.gz "https://get.cryosparc.com/download/worker-latest/$CRYOSPARC_LICENSE_ID"
+if [ $? -ne 0 ]; then
+    echo "Download failed. Please check your license ID and internet connection."
+    return 1
+fi
+
+echo "Extracting CryoSPARC worker package..."
+tar -xf cryosparc_worker.tar.gz || { echo "Failed to extract package."; return 1; }
+rm cryosparc_worker.tar.gz
+echo "Extraction complete."
+
+cd cryosparc_worker || { echo "Failed to enter cryosparc_worker directory"; return 1; }
+
+echo "Running CryoSPARC worker installer..."
+./install.sh --license "$CRYOSPARC_LICENSE_ID"
diff --git a/scripts/reset_cryosparc_password.sh b/scripts/reset_cryosparc_password.sh
new file mode 100755
index 0000000..251526f
--- /dev/null
+++ b/scripts/reset_cryosparc_password.sh
@@ -0,0 +1,31 @@
+#!/bin/bash
+
+# Prompt for CryoSPARC email
+read -rp "Enter your CryoSPARC email (e.g. your_email@psi.ch): " CRYO_EMAIL
+
+# Prompt for new password (hidden input)
+read -rsp "Enter your new CryoSPARC password: " CRYO_PASSWORD
+echo
+
+# Confirm before executing
+echo "Resetting CryoSPARC password for: $CRYO_EMAIL"
+read -rp "Are you sure you want to proceed? [y/N]: " confirm
+case "$confirm" in
+    [yY][eE][sS]|[yY])
+        ;;
+    *)
+        echo "Operation cancelled."
+        exit 1
+        ;;
+esac
+
+# Run the reset command over SSH
+ssh "$USER@merlin7-cryosparc01.psi.ch" \
+    "cryosparcm resetpassword --email '$CRYO_EMAIL' --password '$CRYO_PASSWORD'"
+
+# Check result
+if [ $? -eq 0 ]; then
+    echo "✅ Password reset successfully."
+else
+    echo "❌ Failed to reset password. Please check your inputs and try again."
+fi