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# CryoSPARC Merlin Scripts # CryoSPARC Merlin 7 lanes
This repository contains CryoSPARC *lanes* tailored for running jobs at PSI using the Merlin 7 system. This repository contains CryoSPARC *lanes* tailored for running jobs at PSI using Merlin 7.
## Installation ## Installation
Clone the repository using Git on **Merlin 7**. This is typically done from within your CryoSPARC installation directory (e.g., `/data/user/<user>/cryosparc/`), though this is not strictly required: Clone the repository using Git on **Merlin 7**. This is typically done from within your CryoSPARC installation directory (e.g., `/data/user/<user>/cryosparc/`):
```bash ```bash
git clone -b merlin7 https://gitea.psi.ch/CLS-IT/merlin-cryosparc.git config git clone -b merlin7 https://gitea.psi.ch/CLS-IT/merlin-cryosparc.git config
```` ````
If you already have cloned this repository, run the following command in your directory CryoSPARC installation directory:
```bash
git pull
```
Next, update all `cluster_info.json` files to reflect the correct worker path by replacing the placeholder `USERNAME`. A helper script is available to do this automatically: Next, update all `cluster_info.json` files to reflect the correct worker path by replacing the placeholder `USERNAME`. A helper script is available to do this automatically:
```bash ```bash
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ssh $USER@merlin7-cryosparc01.psi.ch "connect_new lane_name" ssh $USER@merlin7-cryosparc01.psi.ch "connect_new lane_name"
``` ```
## Updating
To fetch the latest features and bug fixes, update the repository:
```bash
git pull
```
Optionally, you can remove outdated lanes before reconnecting (recommended when updating):
```bash
ssh $USER@merlin7-cryosparc01.psi.ch "cryosparcm cluster remove 'lane_name'"
```
Then reconnect lanes as shown in the installation steps:
```bash
ssh $USER@merlin7-cryosparc01.psi.ch "connect_all"
```
## For Developers ## For Developers
If you're contributing to this repository, install Git filters and hooks by running: If you're contributing to this repository, install Git filters and hooks by running: