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MitchobMitchob
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Merge pull request #2 from supernord/edits
Clean up on structural elements, configs, and content
2 parents c6780bf + 7ce85a2 commit 9ffeb55

20 files changed

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‎Gemfile‎

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source "https://rubygems.org"
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gem "openssl", "~> 3.3.1"
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group :jekyll_plugins do
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gem "github-pages"
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end

‎_config.yml‎

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description: "A guide to accessing and using BioShell, a preconfigured cloud bioinformatics environment on NCI Nirin and ARDC Nectar Research Cloud."
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# Metadata description of the website
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remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@2.5.0
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remote_theme: ELIXIR-Belgium/elixir-toolkit-theme
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theme_variables:
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# biocommons blue

‎_data/sidebars/main.yml‎

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url: /index
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- title: Getting started
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url: /why-bioshell
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- title: Using BioShell
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url: /using-bioshell
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subitems:
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- title: Why BioShell?
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url: /why-bioshell
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subitems:
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- title: What is a virtual machine?
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url: /why-bioshell#what-is-a-vm
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- title: Cloud vs HPC
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url: /why-bioshell#cloud-vs-hpc
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- title: Why BioShell?
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url: /why-bioshell#why-bioshell
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- title: BioShell and HPC
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url: /why-bioshell#bioshell-and-hpc
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- title: Accessing BioShell
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url: /access
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subitems:
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- title: Eligibility and acceptable use
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url: /access#eligibility
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- title: Your access pathway
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url: /access#pathways
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- title: Access duration and renewal
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url: /access#duration
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- title: What does access include?
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url: /access#quotas
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- title: Acceptable use policy and service terms
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url: /aup
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subitems:
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- title: Acceptable use
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url: /aup#acceptable-use
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- title: Service commitments
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url: /aup#service-commitments
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- title: Privacy and data collection
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url: /aup#privacy
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- title: Choosing an environment size
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url: /flavours
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subitems:
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- title: A familiar starting point
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url: /flavours#familiar-starting-point
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- title: Small — light preprocessing
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url: /flavours#small
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- title: Medium — scRNA-seq and notebooks
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url: /flavours#medium
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- title: Large — variant calling and HPC-scale
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url: /flavours#large
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- title: Not sure? Start small.
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url: /flavours#start-small
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- title: Quick reference
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url: /flavours#quick-reference
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- title: Further reading
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url: /flavours#further-reading
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- title: Connecting to BioShell
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url: /connecting
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subitems:
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- title: SSH key generation guide
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url: /ssh-keys
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- title: Connect via SSH
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url: /connecting#ssh-connect
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- title: Interactive environments
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url: /connecting#interactive-envs
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- title: First login
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url: /connecting#first-login
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subitems:
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- title: CVMFS access
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url: /connecting#cvmfs-access
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- title: Storage volumes
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url: /connecting#storage
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- title: Using BioShell
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url: /using-bioshell
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subitems:
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- title: Tools and reference data
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url: /tools
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subitems:
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- title: How the tooling stack works
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url: /tools#tooling-stack
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subitems:
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- title: CVMFS
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url: /tools#cvmfs
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- title: sHPC
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url: /tools#shpc
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- title: Shelley-Bio
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url: /tools#shelley-bio
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- title: Installing tools
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url: /tools#installing-tools
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subitems:
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- title: "Recommended: Shelley-Bio"
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url: /tools#bio-shelley
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- title: Why Shelley-Bio over manual sHPC?
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url: /tools#why-shelley
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- title: "Advanced: manual installation"
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url: /tools#shpc-manual
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- title: Loading modules
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url: /tools#load-tool
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- title: Reference datasets
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url: /tools#reference-data
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- title: Troubleshooting
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url: /tools#troubleshooting
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- title: Further reading
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url: /tools#further-reading
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- title: Interactive environments
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url: /interactive
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subitems:
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- title: JupyterLab
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url: /interactive#jupyterlab
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- title: RStudio
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url: /interactive#rstudio
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- title: Using Nextflow with CVMFS
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url: /nextflow
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subitems:
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- title: CVMFS containers
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url: /nextflow#cvmfs-containers
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- title: SHPC modules
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url: /nextflow#shpc-module
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- title: BioShell in practice
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- title: BioShell community and outcomes
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url: /community
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subitems:
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- title: Training workshops
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url: /community#training
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- title: Research outcomes
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url: /community#research
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- title: Get involved
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url: /community#get-involved
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- title: For trainers
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url: /training-development
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subitems:
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- title: VM setup and access
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url: /training-development#vm-setup
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subitems:
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- title: Accessing RStudio and JupyterLab
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url: /training-development#ports
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- title: Developing training materials
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url: /training-development#developing-materials
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subitems:
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- title: Disk budget
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url: /training-development#disk-budget
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- title: Using CVMFS resources
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url: /training-development#cvmfs
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- title: RStudio and JupyterLab environments
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url: /training-development#interactive-envs
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- title: Non-CVMFS resources
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url: /training-development#non-cvmfs
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- title: Trainee directory layout
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url: /training-development#directory-layout
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- title: Pre-snapshot requirements
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url: /training-development#pre-snapshot
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subitems:
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- title: Cloud-init check
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url: /training-development#cloud-init
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- title: Pre-snapshot checklist
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url: /training-development#checklist
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- title: About
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url: /about
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subitems:
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- title: How to cite and acknowledge
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url: /about#cite
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- title: Contributors
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url: /about#contributors
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- title: Acknowledgements
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url: /about#acknowledgements
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- title: References
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url: /about#references
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- title: Get involved
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url: /contributing
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- title: Contributors
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url: /contributors
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- title: Acceptable use policy and service terms
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url: /aup

‎_includes/section-navigation-tiles_mod.html‎

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{%- assign pages_to_add_as_tiles = site.pages -%}
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<div class="page-tiles">
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<div class="page-tiles-container">
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<div class="page-tiles-list">
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{%- for page in pages_to_add_as_tiles -%}
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{%- if page.type == include.type %}
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<a href="{{ page.url | relative_url }}" class="page-tile-link">
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<div class="page-tile-item">
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<div class="page-tile-content">
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<h3 class="page-tile-title" style="margin-top: 0.0rem">{{ page.title }}</h3>
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{% if page.description %}
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<p class="page-tile-description">{{ page.description }}</p>
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{% endif %}
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</div>
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</div>
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</a>
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{% endif %}
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{%- endfor -%}
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</div>
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</div>
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</div>
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<style>
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.page-tiles-list {
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display: grid;
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grid-template-columns: repeat(auto-fill, minmax(300px, 1fr));
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gap: 20px;
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}
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.page-tile-link {
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text-decoration: none;
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color: inherit;
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display: flex;
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}
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.page-tile-item {
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border-radius: 12px;
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padding: 25px;
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transition: all 0.3s ease;
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background: #f0f3fa;
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width: 100%;
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display: flex;
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flex-direction: column;
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justify-content: space-between;
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border: 1px solid #ffffff;
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color: #012152;
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}
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.page-tile-item:hover {
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background: #012152;
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color: #ffffff;
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transform: translateY(-4px);
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box-shadow: 0 8px 25px rgba(0,0,0,0.1);
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border: 1px solid #000000;
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}
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.page-tile-title {
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color: inherit;
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font-size: 1.3rem;
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font-weight: 600;
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margin-bottom: 8px;
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}
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.page-tile-description {
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color: inherit;
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font-size: 0.9rem;
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line-height: 1.5;
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flex-grow: 1;
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}
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</style>

‎_includes/tiles-simple.html‎

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{%- if include.yaml %}
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{%- assign tiles = site.data.tiles[include.target] %}
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{% else %}
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{%- assign tiles = page[include.target] %}
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{%- endif %}
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<div class="simple-tiles">
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<div class="simple-tiles-container">
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<div class="simple-tiles-list row row-cols-1 row-cols-md-2 row-cols-lg-{{ include.col | default: 2 }} gy-2 gx-4">
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{%- for item in tiles %}
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{%- if item.title %}
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<a href="{{ item.url | relative_url }}" class="simple-tile-link">
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<div class="simple-tile-item">
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<div class="simple-tile-content">
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<p class="simple-tile-title" style="font-size: 1.3rem; text-align: center">{{ item.title }}</p>
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</div>
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</div>
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</a>
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{%- endif %}
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{%- endfor %}
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</div>
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</div>
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</div>
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<style>
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.simple-tile-link {
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text-decoration: none;
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color: #012152;
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display: flex;
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}
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.simple-tile-item {
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border-radius: 12px;
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padding: 25px;
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transition: all 0.3s ease;
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background: #f0f3fa;
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width: 100%;
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display: flex;
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flex-direction: column;
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justify-content: space-between;
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color: #012152;
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}
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.simple-tile-item:hover {
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transform: translateY(-4px);
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box-shadow: 0 8px 25px rgba(0,0,0,0.1);
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border-color: #012152;
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background: #012152;
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color: #fff;
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}
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.simple-tile-title {
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color: inherit;
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font-weight: 400;
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margin-top: 0px;
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margin-bottom: 0px;
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}
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</style>

‎contributing.md‎

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---
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title: Contributing
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toc: false
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---
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## Get involved {#get-involved}
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### Run a workshop
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Contact the [**BioCommons Training Team**](https://www.biocommons.org.au/event-support) to deliver a BioShell-powered training event at your institution.
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### Share your work
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If you have published research or training materials using BioShell, [**let us know**](mailto:comms@biocommons.org.au) so we can feature it here.
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### Contribute
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Visit the [**BioShell GitHub repository**](https://github.com/AustralianBioCommons/BioShell) to report issues or contribute to development.

‎index.md‎

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<a href="[PLACEHOLDER — Google Form link to be added]" class="btn btn-primary btn-lg" style="padding: 0.85rem 3rem; font-size: 1.15rem; border-radius: 4px;">Request access</a>
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</p>
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## Getting started
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{% include section-navigation-tiles.html type="Getting started" col="3" %}
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{% include section-navigation-tiles_mod.html type="Getting started" col="1" %}
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2020

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## Using BioShell
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{% include section-navigation-tiles.html type="Using BioShell" col="4" %}
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{% include section-navigation-tiles_mod.html type="Using BioShell" col="3" %}
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## Support
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> **BioShell how-to guide**. Australian BioCommons.
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> [AUTHOR TO SUPPLY — Zenodo DOI once minted]
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## Operational partners
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