Database Curation & Loading Training — 1k1RG (June 3–4, 2026)

Static materials repository for the two-day hands-on training workshop. The live site is served via GitHub Pages from the /docs folder.

Live URL pattern:

https://[ORG].github.io/trainingDatabase/

Replace [ORG] with the GitHub organisation or username that owns this repository.

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Repository layout

trainingDatabase/
├── docs/                  ← GitHub Pages root — everything served from here
│   ├── .nojekyll          ← Disables Jekyll so files are served verbatim (do not delete)
│   ├── index.html         ← Landing page — start here
│   ├── day1/              ← Day 1 session pages (01–10)
│   ├── day2/              ← Day 2 session pages (11–15)
│   ├── cheatsheets/       ← Printable reference cards (PDF or .md placeholders)
│   ├── scripts/           ← Shell and SQL scripts used in the labs
│   └── data/              ← Sample data files for exercises
└── README.md              ← This file (for the organizing team)

All participant-facing content lives inside /docs so GitHub Pages can serve it. All internal links in the HTML files are relative (no leading /), which is required for the site to work correctly under the /<repo>/ subpath on GitHub Pages.

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Enabling GitHub Pages

1. Go to Settings → Pages in the GitHub repository.
2. Under Source, select Deploy from a branch.
3. Branch: main, Folder: /docs.
4. Click Save. The site will be live within ~60 seconds.
5. The URL will be shown on the same Settings → Pages screen.

Important — .nojekyll: The file docs/.nojekyll disables Jekyll processing so every file and folder (including those starting with a digit like 01-orientation.html) is served exactly as named, with no build step. Do not delete this file.

Important — relative links: Every internal href in the HTML files uses a relative path (e.g. day1/03-linux-basics.html, ../scripts/setup.sh). Never add a leading / to an internal link; a project Pages site lives under /<repo>/, not the domain root, so absolute-path links will 404.

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How to update materials

SLIDES (replacing a session placeholder)

Option A — PDF export (simplest):

1. Open your slides in PowerPoint or Google Slides.
2. Export: File → Download → PDF Document.
3. Name the file using the session number convention, e.g., 03-linux-basics-slides.pdf.
4. Place it in the correct folder: docs/day1/ or docs/day2/.
5. Edit the session HTML page (e.g., docs/day1/03-linux-basics.html) — replace the <div class="slide-box"> placeholder block with a link:

   <p><a href="03-linux-basics-slides.pdf" target="_blank">📄 Open Slides (PDF)</a></p>

6. Commit and push. The PDF is served directly from GitHub Pages.

Option B — Self-contained HTML export (allows in-browser slide playback):

1. In Google Slides: File → Download → Web page (.html, .zip).
2. Unzip and rename the folder, e.g., 03-linux-basics-slides/.
3. Place the folder in docs/day1/.
4. Link from the session page to 03-linux-basics-slides/index.html.
5. Test offline: open docs/day1/03-linux-basics.html locally and click the link.

Option C — Embed a Google Slides published link:

1. In Google Slides: File → Share → Publish to web → Embed.
2. Copy the <iframe> snippet.
3. Paste it into the session HTML page, replacing the placeholder div.
4. Note: this requires internet access during the training.

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HTML SESSION PAGES

Each session file is a self-contained HTML file with inline CSS — no build step needed.

1. Open the relevant file, e.g., docs/day1/04-sql-basics.html, in any text editor.
2. Edit the content inside the <main> section.
3. Save. Commit and push.

To add a speaker note or lab instruction, add them inside a <div class="card"> block (the styling is already defined inline in each page).

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CHEAT SHEETS

The cheat sheets are currently .md placeholder files. The download links have been removed from docs/index.html until the PDFs are ready. To restore them:

1. Design or typeset the cheat sheet in your tool of choice (Word, Canva, InDesign, etc.) using the content in docs/cheatsheets/psql-commands.md and docs/cheatsheets/linux-survival.md.
2. Export as PDF.
3. Name the files exactly: psql-commands.pdf and linux-survival.pdf.
4. Place the PDFs in docs/cheatsheets/.
5. Add the download links back to the materials grid in docs/index.html:

   <a class="material-item" href="cheatsheets/psql-commands.pdf" download>
     <div class="material-icon">🐘</div>
     <h4>psql Commands</h4>
     <span>Cheat Sheet (PDF)</span>
   </a>
   <a class="material-item" href="cheatsheets/linux-survival.pdf" download>
     <div class="material-icon">💻</div>
     <h4>Linux Survival</h4>
     <span>Cheat Sheet (PDF)</span>
   </a>

6. Commit and push.

Printing tip: Print double-sided, landscape, one sheet per participant. Laminate if reusing across multiple trainings.

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SCRIPTS

Scripts live in docs/scripts/ and are served directly by GitHub Pages. Each has a header comment describing its purpose and TODO lines marking what needs to be replaced before use.

File	Purpose
setup.sh	Environment setup for participants
load_template.sql	Bulk-loading template (\COPY commands)
pipeline_vcf_to_hdf5.sh	Full VCF → HDF5 pipeline wrapper
vcftomatrix.sh	Extracts genotype matrix from a VCF file
make_HDF_dataset.sh	Converts tabular matrix files to HDF5

1. Edit each script in docs/scripts/ as needed.
2. Remove or replace any TODO placeholder lines with real commands.
3. Test locally before the training (see Pre-Training Checklist).
4. Commit and push.

Pages download links (participants can click these from the landing page or wget them):

https://[ORG].github.io/trainingDatabase/scripts/setup.sh
https://[ORG].github.io/trainingDatabase/scripts/load_template.sql
https://[ORG].github.io/trainingDatabase/scripts/pipeline_vcf_to_hdf5.sh
https://[ORG].github.io/trainingDatabase/scripts/vcftomatrix.sh
https://[ORG].github.io/trainingDatabase/scripts/make_HDF_dataset.sh

Raw GitHub fallback (works even if Pages is not yet enabled):

https://raw.githubusercontent.com/[ORG]/trainingDatabase/main/docs/scripts/setup.sh

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DATA FILES

Data files live in docs/data/ and are served directly by GitHub Pages.

File	Purpose
sample_accessions.csv	10 placeholder rows for bulk-loading exercises
chado_dump.sql	PostgreSQL Chado database dump (used in lab 07)
demo.tar.gz	Hands-on demo archive for pipeline labs
VCFv4.2.pdf	Official VCF v4.2 format specification (reference)

To replace sample_accessions.csv with real training data:

1. Prepare your CSV with the same column headers (or update the SQL template to match).
2. Overwrite docs/data/sample_accessions.csv.
3. Update any references in docs/scripts/load_template.sql (\COPY path).
4. Commit and push.

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Generating the "Download Everything" ZIP

Option A — GitHub automatic ZIP (no extra work): The link in docs/index.html points to:

https://github.com/[ORG]/trainingDatabase/archive/refs/heads/main.zip

This always gives participants the latest state of the main branch as a ZIP. Update the [ORG] placeholder in docs/index.html once.

Option B — Tagged release ZIP (recommended for a fixed training snapshot):

1. Once all materials are final, create a release:

   git tag v2026-06-training
   git push origin v2026-06-training

2. Go to GitHub → Releases → Draft a new release → select the tag.
3. Attach any extra binary files (e.g., the database dump, large PDFs) as release assets.
4. Publish. The release page has a "Source code (zip)" download.
5. Update the ZIP link in docs/index.html to point to the release:

   https://github.com/[ORG]/trainingDatabase/releases/download/v2026-06-training/trainingDatabase-v2026-06-training.zip
   

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File naming convention

Session pages are numbered with a two-digit prefix so they sort correctly in file browsers:

NN-topic-slug.html

• NN — two-digit session number (01–15, matching the schedule order).
• topic-slug — short lowercase kebab-case description of the session.

Do not skip numbers or reuse them. If a session is removed, leave a gap (don't renumber the remaining files, as that would break existing links).

Slide exports and lab worksheets follow the same prefix:

03-linux-basics-slides.pdf
03-linux-basics-lab.pdf

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Pre-Training Checklist

Run through this 48 hours before the training.

Site & links

• Replace [ORG] placeholder in docs/index.html (header link, ZIP link, scripts links)
• GitHub Pages is enabled and the live URL loads correctly
• All 15 session links on the index page open the correct pages
• Each session page opens standalone (no broken CSS, no external dependencies)
• ZIP download link produces a valid archive

Content

• All slide placeholders have been replaced with real PDFs or HTML exports
• Lab worksheets are in place (or embedded in session HTML pages)
• All scripts in docs/scripts/ have TODO lines replaced with real commands
• sample_accessions.csv contains the intended training data
• Cheat sheet PDFs added to docs/cheatsheets/ and download links restored in index.html

USB backup

• Clone or download the full repository as a ZIP
• Unzip onto the USB drive, keeping the directory structure intact
• Open docs/index.html from the USB in a browser — all links should work offline
• Copy the database dump file onto the USB as well
• Label the USB drives with the training name and date

Printing

• Print cheat sheets (one per participant, double-sided landscape)
• Print lab worksheets (if not embedded in the HTML pages)
• Test that the index page is readable on a projector at 1920×1080 from 5 m away

On the day

• Distribute USB drives at the start of Day 1
• Confirm Wi-Fi credentials are working for all participants
• Have a fallback plan if the projector resolution differs (the site is responsive)