03_create-exp-repo.qmd

---
title: "Creating an experiment repo"
engine: knitr
---

```{bash echo = F, eval = T}
rm -rf experiment_repo
```

## Overview

We use the term "experiment repo" for a git repository that 
contains the plumbing required for a numerical experiment. 

It consists in a git repository with:

- the `nextflow` executable and its configuration, `nextflow.config`;
- a git submodule, `nf-nest` containing useful tools; 
- your `.nf` files and other supporting files. 

This pages explains how to setup an experiment repo.


## Location 

In an HPC context, the experiment repo should be in a read/write location accessible to all nodes. 

For example, on Sockeye the first choice if you allocation has it would be to use burst storage, i.e. cd to a path of the form

```bash
export JULIA_DEPOT_PATH=/arc/burst/[allocation_code]/[username_in_alloc]/
```

A second choice would be to use the scratch space, i.e. cd to a path of the form

```bash
export JULIA_DEPOT_PATH=/scratch/[allocation_code]/[username_in_alloc]/
```


## Instructions {#sec-instructions}

For quick setup, run the following commands:

```{bash output = F}
#| eval: true
#| file: create-exp-repo.sh
```