This lesson is being piloted (Beta version)

Intermediate Programming with Python: Setup

Add anaconda to your gitbash $PATH

  1. Open git bash

  2. Run the following command: export PATH=$PATH:~/AppData/Local/Continuum/anaconda3/Scripts

  3. Run the following command: source activate

Now you are good to go!

Sample Data

This lesson uses an example fastq file. Inside your dataschool folder, please make yourself the following directory structure:

python/data

Download the following files to this directory:

a_few_lines_of_text.txt

sample.fastq

Installing Anaconda

CSIRO-specific instructions

  1. The Anaconda Python distribution can be installed from the CSIRO IM&T Software Centre.
  2. A full guide to using the Software Centre is here.
  3. Open the Software Centre.
  4. When the Software Centre opens, search for “anaconda” and install “Anaconda Python 3”.

Get Help from IM&T

You can get help from the IM&T Service Desk if you require help with installing Anaconda onto a CSIRO computer.

For Everyone Else

  1. Visit the Anaconda download page.
  2. Select your operating system (Windows, macOS, or Linux).
  3. Download the Python 3.7 64-bit graphical installer.
  4. After the download completes, run the installer to install Anaconda.

Follow the Installation Guide

If you need more detailed guidance, then please follow the Anaconda Installation guide.

Updating Anaconda

  1. Once Anaconda is installed, it is a good idea to update it.
  2. The article Keeping Anaconda Up To Date is a good guide to updating Anaconda after it is installed.
  3. It boils down to opening an Anaconda terminal and running the command: 
    conda update --all

Updating is not essential for this course

If you would rather skip updating, then it is not essential for this course.