Sirota Lab — Progressive, Reproducible Workflow Bootcamp

# Bootcamp II
### *Snakebids*

---

## Tutorial Overview

1. VSCode SSH Workspace
2. Terminal Setup
3. explore `sirocampus` and install `ds-bidsmini`
4. Part I: Snakemake
5. Part II: Snakebids

---

## 1. VSCode SSH Workspace

---

### 1.0 Open VSCode

Press

```
Ctrl + Shift + P
```

A command box will appear.

---

### 1.1 Connect via Remote-SSH

Type and select:

```
Remote-SSH: Connect to Host...
```

Enter your host: beta

If no hosts are being shown then type:
```bash
<user>@beta
```

Enter your **password** when prompted.

---

### 1.2 Create a tutorial folder

Open VSCode terminal

```bash
Ctrl + J
```

In the VSCode terminal, run:

```bash
# I have mine under
snakebidsdir="/storage2/arash/tutorials/snakebids"

snakebidsdir="/path/to/.../tutorials/snakebids"

mkdir -p $snakebidsdir

# change dir
cd $snakebidsdir
```

copy the absolute path to `snakebids` directory (without quotation marks)

---

### 1.3 VSCode: Open Folder

Select:

```
Open Folder
```

By default, `/home/<user>` will appear. Replace it by pasting the absolute path of the `snakebids` folder.

When prompted, select:

> ✅ Yes, I trust the authors

---

### 1.4 VSCode: panels
toggle File explorer
```
Ctrl + B
```
toggle terminal
```
Ctrl + J
```

---

![[_shared/fragments/terminal-setup/section-heading.md]]

---

![[_shared/fragments/terminal-setup/umask.md]]

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![[_shared/fragments/terminal-setup/alias-riastoreshared.md]]

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![[_shared/fragments/terminal-setup/bashrc-includes.md]]

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![[_shared/fragments/terminal-setup/conda-shared-alias.md]]

---

![[_shared/fragments/terminal-setup/reload-and-activate.md]]

---

## 3.  `sirocampus`

---

### 3.0 Clone `sirocampus`

```bash
# navigate to your base folder
cd /storage<storage-number>/<name>/
# mine is: /storage2/arash
```

install the `sirocampus`:

```bash
datalad install -s "ria+file://$riastoreshared#~sirocampus" sirocampus
```

---

### 3.1 `sirocampus` tree

run:
```bash
tree -L 3 sirocampus
```

output:
```bash
```bash
sirocampus (the sirotalab super repository)
├── bib 
│   └── ...
├── data
│   └── ...
├── docs
│   └── ...
└── code
    └── ...
```

---

### 3.1 `sirocampus` tree

```bash
```bash
sirocampus
├── bib (lab paper pool > linked with Zotero)
│   ├── metadata
│   └── pdfs
├── data
│   └── ...
├── docs
│   └── ...
└── code
    └── ...
```

run:
```bash
cd sirocampus
datalad get -n bib
```

---

### 3.2 `sirocampus:bib`

run:
```bash
ls -l bib/pdfs/
```

to download a paper, run:
```bash
datalad get bib/pdfs/<paper name>
```

---

### 3.3 `sirocampus:data`

```bash
sirocampus (the sirotalab super repository)
├── bib (lab paper pool > linked with Zotero)
├── data (datalad superdataset containing all sirota lab datasets)
│   ├── ds-bidsmini
│   ├── ds-msol
│   ├── ds-gecog
│   ├── ds-pixecog
│   └── ... 
├── docs
│   └── ...
└── code
    └── ...
```

---

### 3.3 `sirocampus:data`

```bash
sirocampus (the sirotalab super repository)
├── bib (lab paper pool > linked with Zotero)
├── data (datalad superdataset containing all sirota lab datasets)
│   ├── ds-bidsmini
│   ├── ds-msol
│   ├── ds-gecog
│   ├── ds-pixecog
│   └── ... To be added by you 🎨! 
├── docs
│   └── ...
└── code
    └── ...
```

---

### 3.4 `sirocampus:docs`

Diataxis framework: https://diataxis.fr/

two axes:
cognition -> action
acquisition -> application

widely adopted by tools for documentation (e.g. pytest, ...)

---

### 3.4 `sirocampus:docs`

```bash
```bash
sirocampus (the sirotalab super repository)
├── bib 
├── data
├── docs (lab documents based on Diataxis framework)
│   ├── logs
│   ├── how-to
│   ├── reference
│   ├── tutorials > snakebids.md
│   └── explanation
└── code
    └── ...
```

### 3.4 `sirocampus:docs` lab wiki

easy contribution to lab wiki

```bash
```bash
sirocampus (the sirotalab super repository)
├── bib 
├── data
├── docs (lab documents based on Diataxis framework)
│   ├── wiki (markdown version of all lab dokuwiki files)
│   ├── logs
│   ├── how-to
│   ├── reference
│   ├── tutorials > snakebids.md
│   └── explanation
└── code
    └── ...
```

automatic conversion between dokuwiki and markdown formats.

---

### 3.5 `sirocampus:code`

```bash
```bash
sirocampus (the sirotalab super repository)
├── bib 
├── data
├── docs
└── code (sirota lab code)
    ├── lib (library of third-party tools)
    ├── cogpy (ecog package)
    ├── labbox (lab MATLAB toolbox)
    └── labpy (lab Python package)
```

---

### 3.6 `sirocampus` tree

```bash
```bash
sirocampus (the sirotalab super repository)
├── bib (lab paper pool > linked with Zotero)
├── data (datalad superdataset containing all sirota lab datasets)
│   ├── ds-bidsmini
│   ├── ds-msol
│   ├── ds-gecog
│   ├── ds-pixecog
│   └── ... To be added by you 🎨! 
├── docs (lab documents based on Diataxis framework)
│   ├── logs
│   ├── how-to
│   ├── reference
│   ├── tutorials
│   └── explanation
└── code (sirota lab code)
    ├── lib (library of third-party tools)
    ├── cogpy (ecog package)
    ├── labbox (lab MATLAB toolbox)
    └── labpy (lab Python package)
```

---

## 4.  `snakemake`

---

### 4.0 create a mini bids

Create a **tiny BIDS-style dataset** with:

- 2 subjects: `sub-01`, `sub-02`
    
- 2 sessions per subject: `ses-01`, `ses-02`
    
- Small dummy motion CSV files in each session directory

---

# 📁 Desired Structure

```
sub-01/
  ses-01/
    motion/
      sub-01_ses-01_motion.csv
  ses-02/
    motion/
      sub-01_ses-02_motion.csv
sub-02/
  ses-01/
    motion/
      sub-02_ses-01_motion.csv
  ses-02/
    motion/
      sub-02_ses-02_motion.csv
```

---

# ⚙️ Bash Command

```bash
#!/bin/bash
mkdir raw
cd raw

# Create BIDS-like directory structure
for sub in 01 02; do
  for ses in 01 02; do
    mkdir -p sub-${sub}/ses-${ses}/motion
    # Create a tiny dummy motion CSV file (<1MB)
    echo "time,dx,dy,dz,rx,ry,rz" > sub-${sub}/ses-${ses}/motion/sub-${sub}_ses-${ses}_motion.csv
    echo "0,0.1,0.2,0.3,0.01,0.02,0.03" >> sub-${sub}/ses-${ses}/motion/sub-${sub}_ses-${ses}_motion.csv
    echo "1,0.2,0.3,0.4,0.02,0.03,0.04" >> sub-${sub}/ses-${ses}/motion/sub-${sub}_ses-${ses}_motion.csv
  done
done
```

---

# ✅ Result

- Four CSV files created
    
- Each file only a few bytes (tiny)
    
- Ready for testing or demonstration

```
sub-{01,02}/ses-{01,02}/motion/sub-<label>_ses-<label>_motion.csv
```

Perfect — here’s the **ultra-simple single-file Snakemake example**, using literal paths and no lambdas or wildcards.  
It just processes one file: `raw/sub-01/ses-01/motion/sub-01_ses-01_motion.csv`.

---

### 4.1.1 _SingleFile_: Create Snakefile

```bash
# Snakefile (single-file, literal paths only)

configfile: "config.yaml"

rule all:
    input:
        "derivatives/pipeline/sub-01/ses-01/motion/sub-01_ses-01_motion_copy.csv"

rule copy_motion:
    input:
        "raw/sub-01/ses-01/motion/sub-01_ses-01_motion.csv"
    output:
        "derivatives/pipeline/sub-01/ses-01/motion/sub-01_ses-01_motion_copy.csv"
    shell:
        """
        mkdir -p $(dirname {output})
        cp {input} {output}
        echo 'Copied {input} to {output}'
        """
```

---

### 4.1.2 _SingleFile_: Run `snakemake`

```bash
snakemake -c 1
```

This will:

- Create the output folder `derivatives/pipeline/sub-01/ses-01/motion/`
    
- Copy the CSV file from `raw/`
    
- Print a simple confirmation message

---

### 4.1.3 _SingleFile_: Check the logs

under `.snakemake`

---

### 4.1.4 _SingleFile_: Create config file

Include a minimal config file (even if not used much yet):

```bash
# config.yaml
raw_dir: raw
out_dir: derivatives/pipeline
subject: "01"
session: "01"
```

---

### 4.1.5 _SingleFile_: Run `snakemake`

Same simple execution — config is just declared for consistency:

```bash
snakemake -c 1
```

✅ **Result:**  
A working minimal Snakemake pipeline that copies one literal file (`sub-01/ses-01`) from `raw/` to `derivatives/pipeline/`.

---

### 4.2.1 *MultiFile*: Create Snakefile

---

### 4.2.2 *MultiFile*: Run `snakemake`

---

## 4.  `snakebids`

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### 5.1 *snakebids*: Create Snakefile

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### 5.2 *snakebids*: Run `snakemake`

---