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_config.yml
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_config.yml
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###########################################################
### Welcome to Beautiful Jekyll!
### This config file is meant for settings that affect your entire website. When you first
### set up your website you should go through all these settings and edit them, but after
### the initial set up you won't need to come back to this file often.
###########################################################
############################
# --- Required options --- #
############################
# Name of website
title: BABS 3291
# Your name to show in the footer
author: Helen King
###############################################
# --- List of links in the navigation bar --- #
###############################################
navbar-links:
Course Structure: "course_structure"
Practical W1-5:
- Sample Datasets: "practical_overview/sample_datasets"
- Week 1A Setting Up on Katana: "practical_overview/Week1A_SettingUpOnKatana"
- Week 1B Introducing the Shell: "practical_overview/Week1B_Introducing_the_Shell"
- Week 1C Navigating Files and Directories: "practical_overview/Week1C_Navigating_Files_And_Directories"
- Week 1D Writing Scripts and Working with Data: "practical_overview/Week1D_Working_Files_Directories"
- Week 2A Exploring your dataset: "practical_overview/Week2A_Exploring_Dataset"
- Week 2B Redirection: "practical_overview/Week2B_Redirection"
- Week 2C Creating scripts and submitting: "practical_overview/Week2C_Writing_Scripts_workingwithdata"
- Week 3 Using FASTQC For Data Quality Report: "practical_overview/Week3_FASTQC"
- Week 4 Using Trimmomatic for Trimming and Filtering: "practical_overview/Week4_Trimming"
- Week 5 Quiz and Prac Revision: "practical_overview/quiz"
Practical W6-10:
- Week 6 Flexibility Week: "practical_overview/flex_week"
- Week 7 Using Kallisto for Pseudoalignment: "practical_overview/Week7_Alignment"
- Week 8A Using DEGUST for Differential Expression Analysis: "practical_overview/Week8A_Differential_Expression"
- Week 8B Explaining DE Summary: "practical_overview/Week8B_Explaining_DE"
- Week 8C Understanding the Theory Behind Differential Expression Analysis: "practical_overview/Week8C_QC_GO"
Tutorial Overview:
- Week 1: "tutorial_overview/week1"
- Week 2: "tutorial_overview/week2"
- Week 3: "practical_overview/talks"
- Week 4: "tutorial_overview/week4"
- Week 5: "tutorial_overview/week5"
# - Week 6: "tutorial_overview/week6"
# - Week 7: "tutorial_overview/week7"
# - Week 8: "practical_overview/ramachotti_tour"
# - Week 9: "tutorial_overview/week9"
Key Information: "key_info"
################
# --- Logo --- #
################
# Image to show in the navigation bar - works best with a square image
# Remove this parameter if you don't want an image in the navbar
# avatar: "/assets/img/avatar-icon.png"
avatar: "/assets/img/unsw.png"
# By default, the image is cut into a circle. You can disable this behaviour by setting 'round-avatar: false'
round-avatar: false
# If you want to have an image logo in the top-left corner instead of having the title of the website,
# then specify the following parameter
#title-img: /path/to/image
#####################################
# --- Footer social media links --- #
#####################################
# Select the social network links that you want to show in the footer.
# Uncomment the links you want to show and add your information to each one.
# social-network-links:
# email: "someone@example.com"
# rss: true # remove this line if you don't want to show an RSS link at the bottom
# facebook: deanattali
# github: daattali
# twitter: daattali
# patreon: DeanAttali
# youtube: c/daattali
# # medium: yourname
# reddit: yourname
# linkedin: daattali
# xing: yourname
# stackoverflow: "3943160/daattali"
# snapchat: deanat78
# instagram: deanat78
# spotify: yourname
# telephone: +14159998888
# steam: deanat78
# twitch: yourname
# yelp: yourname
# telegram: yourname
# calendly: yourname
# mastodon: instance.url/@username
# ORCID: your ORCID ID
# google-scholar: your google scholar
# discord: invite/invite_code or users/userid
# kaggle: yourname
# hackerrank: yourname
# If you want your website to generate an RSS feed, provide a description
# The URL for the feed will be https://<your_website>/feed.xml
rss-description: This website is the BABS course
###########################
# --- General options --- #
###########################
# Select which social network share links to show in posts
# share-links-active:
# twitter: true
# facebook: true
# linkedin: true
# vk: false
# How to display the link to your website in the footer
# Remove this if you don't want a link in the footer
# url-pretty: "MyWebsite.com"
# Excerpt word length - Truncate the excerpt of each post on the feed page to the specified number of words
excerpt_length: 50
# Whether or not to show an excerpt for every blog post in the feed page
feed_show_excerpt: true
# Whether or not to show a list of tags below each post preview in the feed page
feed_show_tags: true
# Add a search button to the navbar
post_search: true
# Add a button in the footer to edit the current page. Only works if your website is hosted on GitHub
edit_page_button: true
# Allow sub-menu items (second-level navigation menu items) to be longer than the top-level menu
# If this setting is off, then long sub-menu words might get cut off
# See https://github.com/daattali/beautiful-jekyll/issues/765 to understand the issue this setting can solve
navbar-var-length: True
# The keywords to associate with your website, for SEO purposes
#keywords: "my,list,of,keywords"
######################################
# --- Colours / background image --- #
######################################
# Personalize the colours in your website. Colour values can be any valid CSS colour
navbar-col: "#EAEAEA"
navbar-text-col: "#404040"
navbar-border-col: "#DDDDDD"
page-col: "#FFFFFF"
text-col: "#404040"
link-col: "#008AFF"
hover-col: "#0085A1"
footer-col: "#EAEAEA"
footer-text-col: "#777777"
footer-link-col: "#404040"
footer-hover-col: "#0085A1"
# Alternatively, the navbar, footer, and page background can be set to an image
# instead of colour
#navbar-img: "/assets/img/bgimage.png"
#footer-img: "/assets/img/bgimage.png"
#page-img: "/assets/img/bgimage.png"
# Suggest a colour for mobile browsers to use as the browser's theme. This is only supported by a few mobile browsers.
#mobile-theme-col: "#0085A1"
# For any extra visual customization, you can include additional CSS files in every page on your site. List any custom CSS files here
#site-css:
# - "/assets/css/custom-styles.css"
# If you have common JavaScript files that should be included in every page, list them here
#site-js:
# - "/assets/js/custom-script.js"
#################################
# --- Web Analytics Section --- #
#################################
# Fill in your Google Analytics gtag.js ID to track your website using gtag
#gtag: ""
# Fill in your Google Analytics ID to track your website using Google Analytics
#google_analytics: ""
# Fill in your Cloudflare Analytics beacon token to track your website using Cloudflare Analytics
#cloudflare_analytics: ""
# Google Tag Manager ID
#gtm: ""
# Matomo (aka Piwik) Web statistics
# Uncomment the following section to enable Matomo. The opt-out parameter controls
# whether or not you want to allow users to opt out of tracking.
#matomo:
# site_id: "9"
# uri: "demo.wiki.pro"
# opt-out: true
####################
# --- Comments --- #
####################
# To use Disqus comments, sign up to https://disqus.com and fill in your Disqus shortname (NOT the userid)
#disqus: ""
# To use Facebook Comments, create a Facebook app and fill in the Facebook App ID
#fb_comment_id: ""
# To use CommentBox, sign up for a Project ID on https://commentbox.io
#commentbox: "" # Project ID, e.g. "5694267682979840-proj"
# To use Utterances comments: (0) uncomment the following section, (1) fill in
# "repository" (make sure the repository is public), (2) Enable Issues in your repository,
# (3) Install the Utterances app in your repository https://github.com/apps/utterances
# See more details about the parameters below at https://utteranc.es/
#utterances:
# repository: # GitHub username/repository eg. "daattali/beautiful-jekyll"
# issue-term: title # Mapping between blog posts and GitHub issues
# theme: github-light # Utterances theme
# label: blog-comments # Label that will be assigned to GitHub Issues created by Utterances
# To use Staticman comments, uncomment the following section. You may leave the reCaptcha
# section commented if you aren't using reCaptcha for spam protection.
# Using Staticman requires advanced knowledge, please consult
# https://github.com/eduardoboucas/staticman/ and https://staticman.net/ for further
# instructions. For any support with staticman please direct questions to staticman and
# not to BeautifulJekyll.
#staticman:
# repository : # GitHub username/repository eg. "daattali/beautiful-jekyll"
# branch : master # If you're not using `master` branch, then you also need to update the `branch` parameter in `staticman.yml`
# endpoint : # URL of your deployment, with a trailing slash eg. "https://<your-api>/v3/entry/github/"
# reCaptcha: # (optional, set these parameters in `staticman.yml` as well)
# siteKey : # You need to apply for a site key on Google
# secret : # Encrypt your password by going to https://<your-own-api>/v3/encrypt/<your-site-secret>
# To use giscus comments:
# (0) Uncomment the following giscus section, (1) Enable Discussions in your GitHub repository,
# (2) Install the giscus app in your repository (details at https://giscus.app),
# (3) Fill in *all* the parameters below
# See more details about giscus and each of the following parameters at https://giscus.app
#giscus:
# hostname: giscus.app # Replace with your giscus instance's hostname if self-hosting
# repository: # GitHub username/repository eg. "daattali/beautiful-jekyll"
# repository-id: # ID of your repository, retrieve this info from https://giscus.app
# category: Announcements # Category name of your GitHub Discussion posts
# category-id: # ID of your category, retrieve this info from https://giscus.app
# mapping: pathname
# reactions-enabled: 1
# emit-metadata: 0
# theme: light
################
# --- Misc --- #
################
# Ruby Date Format to show dates of posts
date_format: "%B %-d, %Y"
# Facebook App ID
#fb_app_id: ""
#################################################################################
# --- You don't need to touch anything below here (but you can if you want) --- #
#################################################################################
# Output options (more information on Jekyll's site)
timezone: "Australia/Sydney"
markdown: kramdown
highlighter: rouge
permalink: /:year-:month-:day-:title/
paginate: 5
kramdown:
input: GFM
# Default YAML values (more information on Jekyll's site)
defaults:
-
scope:
path: ""
type: "posts"
values:
layout: "post"
comments: true # add comments to all blog posts
social-share: true # add social media sharing buttons to all blog posts
-
scope:
path: "" # any file that's not a post will be a "page" layout by default
values:
layout: "page"
# Exclude these files from production site
exclude:
- CHANGELOG.md
- CNAME
- Gemfile
- Gemfile.lock
- LICENSE
- README.md
- screenshot.png
- docs/
plugins:
- jekyll-paginate
- jekyll-sitemap
# Beautiful Jekyll / Dean Attali
# 2fc73a3a967e97599c9763d05e564189