How to Edit This Wiki

This wiki is powered by DokuWiki. It is an open platform where ABI members can contribute documentation. Currently, editing does not require logging in – this may change in the future.

There are two ways to create a new page:

Method 1: Search and Create

1. Search for the topic in the search bar.
2. If the page does not exist, you will see a “Create this page” button on the right side.
3. Click it to start editing.

Method 2: Direct URL

1. Navigate to the desired URL directly. For example, to create a page software:bwa, go to https://wiki.abi.am/software:bwa.
2. Click “Create this page” to start writing.

1. Navigate to the page you want to edit.
2. Click the “Edit this page” button (pencil icon) in the toolbar.
3. Make your changes.
4. Click “Save” to publish immediately, or “Preview” to review first.

DokuWiki organizes pages into namespaces, which work like folders. The colon (:) separates namespace levels.

Examples:

• software:slurm – the “slurm” page inside the “software” namespace.
• getting_started:new_member – the “new_member” page inside “getting_started”.
• infra:ldap – the “ldap” page inside “infra”.

Each namespace should have a start page that serves as the landing/index page for that section. For example, software:start is the main page for the Software section.

Current namespaces on this wiki:

When creating a new page, always place it in the appropriate namespace rather than at the root level.

DokuWiki uses its own simple markup syntax. Here are the essentials:

====== Heading 1 ======
===== Heading 2 =====
==== Heading 3 ====

**bold text**
//italic text//
''monospaced text''

  * Bullet list item
  * Another item
    * Nested item

  - Numbered list
  - Second item

[[namespace:page|Link Text]]
[[https://example.com|External Link]]

^ Header 1 ^ Header 2 ^
| Cell 1   | Cell 2   |
| Cell 3   | Cell 4   |

Use <code> tags for code blocks. You can specify the language for syntax highlighting:

<code bash>
#!/bin/bash
echo "Hello World"

</code>

*TODO: If you have the “note” or “wrap” plugin installed, document it here. Otherwise, you can use bold text or blockquotes:*

> **Note:** This is an important note.

> **Warning:** Be careful with this operation.

For the complete syntax guide, see:

• ABI Wiki Syntax Reference (local copy)
• Official DokuWiki Syntax Guide

All edits are saved. You can view and restore previous versions of any page:

1. Click the “Old revisions” button on any page.
2. Compare versions to see what changed.
3. Revert to a previous version if needed.

To see an overview of all pages organized by namespace, visit the Sitemap.

• Use the right namespace. Put your page in the correct section (software, pipelines, infra, etc.).
• Use descriptive page names. Use lowercase with underscores: variant_calling, not VariantCalling or Variant Calling.
• Add a table of contents. DokuWiki auto-generates one for pages with 3+ headings.
• Link to related pages. Use [[namespace:page|Description]] to cross-reference.
• Include examples. Code blocks with real commands are more useful than abstract descriptions.
• Sign your work (optional). Add your name or initials at the bottom if you want others to know who to ask.

If you are unsure where to put something or how to format it, contact it-support@abi.am or just create the page – someone will help reorganize it if needed.