# v1 VM Deployment (LeafWeb Layout)

This branch configures PISCAL for deployment on a VM matching the layout used by `piscal.eastus.cloudapp.azure.com`, so the LeafWeb client can access jobs and storage at the expected paths.

## Directory Layout

```
/home/piscaladmin/
├── LeafWeb/                      # Scripts + project directories
│   ├── piscal_launcher.cfg       # Config (piscal_executable, storage paths)
│   ├── piscal_launcher.sh
│   ├── piscal_manager.sh
│   ├── subdir_year.sh
│   ├── README.txt
│   ├── 280_CinnamomumbodinieriLévl/   # Project dirs (input/, output/, run/, etc.)
│   ├── 311_AnnaAsaday3high/
│   └── ...
├── LeafWeb_storage/              # Shared storage for client
│   ├── input/
│   └── output/
├── piscal/                       # Source (optional)
└── piscal_executable/            # Compiled binary
    └── piscal
```

## Deployment

**Docker (recommended):** The Docker image uses this layout by default. See [README-Docker.md](README-Docker.md).

**Manual VM deployment:** Copy scripts to LeafWeb and the compiled `piscal` binary to `piscal_executable/`:

```bash
ssh piscaladmin@host 'mkdir -p ~/LeafWeb ~/piscal_executable ~/LeafWeb_storage/input ~/LeafWeb_storage/output'
scp piscal-manager/*.cfg piscal-manager/*.sh piscal-manager/README.txt piscaladmin@host:~/LeafWeb/
scp leafres/testrun/piscal piscaladmin@host:~/piscal_executable/
ssh piscaladmin@host 'chmod +x ~/LeafWeb/*.sh'
```

## Configuration

`piscal_launcher.cfg` uses VM paths:

- `piscal_executable="/home/piscaladmin/piscal_executable/piscal"`
- `storage_directory="/home/piscaladmin/LeafWeb_storage"`

Adjust if your VM uses different locations.

## Running Jobs

From `~/LeafWeb`:

```bash
cd ~/LeafWeb
./piscal_manager.sh -d 280_CinnamomumbodinieriLévl -s -p C3_photosynthesis_leafweb
./piscal_manager.sh -d 280_CinnamomumbodinieriLévl   # status
./piscal_manager.sh -d 280_CinnamomumbodinieriLévl -c   # cleanup
```

The `-d` argument is the project directory name (a subdir of LeafWeb).