====== How to Edit This Wiki ======

This wiki is powered by [[https://www.dokuwiki.org|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.

===== Creating a New Page =====

There are two ways to create a new page:

**Method 1: Search and Create**
  - Search for the topic in the search bar.
  - If the page does not exist, you will see a "Create this page" button on the right side.
  - Click it to start editing.

**Method 2: Direct URL**
  - Navigate to the desired URL directly. For example, to create a page ''software:bwa'', go to ''%%https://wiki.abi.am/software:bwa%%''.
  - Click "Create this page" to start writing.

===== Editing Existing Pages =====

  - Navigate to the page you want to edit.
  - Click the **"Edit this page"** button (pencil icon) in the toolbar.
  - Make your changes.
  - Click **"Save"** to publish immediately, or **"Preview"** to review first.

===== Namespaces =====

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:

^ Namespace ^ Purpose ^
| ''getting_started'' | Onboarding guides, cluster basics, and this wiki editing guide |
| ''software'' | Documentation for installed software and tools |
| ''pipelines'' | End-to-end bioinformatics workflows |
| ''scripts'' | Reusable individual scripts |
| ''databases'' | Reference genomes, indexes, and shared datasets |
| ''projects'' | Research project documentation |
| ''infra'' | IT infrastructure (servers, network, LDAP, etc.) |

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

===== Formatting Basics =====

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

<code>
====== 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   |
</code>

=== Code blocks ===

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

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

=== Admonitions / Notes ===

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

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

> **Warning:** Be careful with this operation.
</code>

===== Full Syntax Reference =====

For the complete syntax guide, see:
  * **[[wiki:syntax|ABI Wiki Syntax Reference]]** (local copy)
  * [[https://www.dokuwiki.org/wiki:syntax|Official DokuWiki Syntax Guide]]

===== Page History =====

All edits are saved. You can view and restore previous versions of any page:
  - Click the **"Old revisions"** button on any page.
  - Compare versions to see what changed.
  - Revert to a previous version if needed.

===== Sitemap =====

To see an overview of all pages organized by namespace, visit the [[?do=index|Sitemap]].

===== Guidelines for Contributors =====

  * **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.

===== Need Help? =====

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