getting-started

Introduction

1. Discuss with your supervisor regarding which compute environment is most sustainable
2. Email EL for account
3. Login BCCDC's Posit workbench More screenshots
4. Choose File > New > Terminal

By default, Posit uses Python 3.6. To check available versions, copy-paste:

ls -1d /opt/python/*

Use cases

Scenario 1: Reproducing environment from Python Git repo (created by your peers)

Part 1. Clone

1. Navigate to the location where you plan to save your work, e.g., create a folder called DSI in your home directory $HOME

   mkdir $HOME/DSI
   cd $HOME/DSI   
   

2. Clone the repository:

   git clone https://github.com/BCCDC-DSI/RADD.git
   

3. Optional, list the items in the repo

   cd RADD
   ls -lstr 
   

Part 2. Build

1. Navigate to the location where your requirements.txt is saved; e.g.

   cd $HOME/DSI/RADD/workflows/part2_version2
   

2. Create a virtual environment (VE). Three options:

   Option A:

   conda create --name raddpt2 python=3.12   
   

   Option B: Store the VE under your folder

   mkdir $HOME/myvenv/
   conda create --prefix $HOME/myvenv/raddpt2 python=3.12  
   

   Option C: Build without use of conda

   python3 -m venv raddpt2
   

3. Activate virtual environment and upgrade pip:

   Option A or B:

   conda activate raddpt2
   conda install pip
   

   Option C:

   source raddpt2\bin\activate
   pip install --upgrade pip
   

4. Build:

   pip install -r requirements.txt
   

Git

1. Configure for the first time

   git config --global user.email "you@example.com"
   git config --global user.name "your_github_username"
   

Conda

Note: conda is not available by default. On 2024-10-03, we were able to download and install:

1. Download miniconda3

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

2. Run the installation script:

bash Miniconda3-latest-Linux-x86_64.sh

3. Optionally, disable the auto-initialization of conda:

conda config --set auto_activate_base false

4. If disabled by default, you would need to activate conda's base environment every time you start new session:

eval "$($HOME/miniconda3/bin/conda shell.bash hook)"

R

Via Launcher

Via terminal

Navigating to data folders

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