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Wiki Help

This wiki is implemented using the MoinMoin wiki software. MoinMoin is a mature, full-featured and widely used wiki package. It is also by far the most popular wiki package written in Python, the Galaxy ecosystem's language of choice.

A wiki is a web site that is meant to be both easy to read, and easy to update. The goal of this wiki is to document all things Galaxy, and to encourage as much contribution from the Galaxy community as possible. This wiki allows users to create logins and edit and add content.

This page has information on how to use this wiki. It describes what you can do in MoinMoin, but not necessarily what you should do. See Wiki Best Practices for our own local best practices and culture.

MoinMoin Help

MoinMoin comes with extensive documentation on how to use it and update it. Some useful links:

Creole Markup

The default markup for this wiki is MoinMoin's.  However, you can also use Creole, which is what was used on the previous Galaxy Wiki.  However, on any single page you can only use one or the other. To use Creole, include this as the top line of the page:

#format text/creole

Things don't work quite as well with creole as they do with MoinMoin syntax, but they work for most things.  See the nwwl Macro if you are having trouble with extraneous BogusLinks (that point to non-existent pages) on your Creole pages.

Attachments

Attachments include things like images, PDFs, and text files.

Where to Put Attachments

Attachments are, well, attached to a specific page. They can be referenced from any page, not just the one they are attached to. We have two suggested places for attaching files:

  1. Attach them to the page that links to them.
  2. Attach them to the appropriate Images or Documents page.

The first approach is simpler, but doesn't lend itself to reuse. The second approach takes more work, but encourages attachment reuse.

Direct Linking to Attachments

The default behavior for attached files is slightly irritating. For example,

MoinMoin Wiki Markup

Result

Comments

[[attachment:Events/GCC2011/AssemblyAndAnnotationUsingGalaxy.pptx|PowerPoint]]

PowerPoint

Goes to an intermediate page that requires another click to download the attachment.

To get rid of that intermediate page and go direct to the download add |do=get to the end of the link:

MoinMoin Wiki Markup

Result

Comments

[[attachment:Events/GCC2011/AssemblyAndAnnotationUsingGalaxy.pptx|PowerPoint|&do=get]]

PowerPoint

Goes straight to download.

Some types of attachments, like PDFs are displayed directly in the wiki window by default. To override that behavior, also add |do=get to the link.

Local Extensions

Point to standard Macros and then enumerate local macros, and CSS here.

Macros

MoinMoin comes with many macros. Macros are shortcuts for doing something in a wiki. This wiki contains all the standard macros, plus some from the MoinMoin Macro Market, and some custom local ones as well. The last two types are described here.

Macro

Description

Example

span

Applies a predefined CSS class (see CSS below) to a span of text. Care must be taken not to cross HTML blocks.

div

Applies a predefined CSS class to an HTML block. Care must be taken so these are not terminated in the middle of HTML block. These can also be nested.

nwwl

MoinMoin's Creole Parser incorrectly converts all sorts of non-WikiName words to links, and often does not handle the Creole WikiName escape character correctly either. When working in Creole, wrap words that you don't want to be links in this macro.

<<nwwl(BLAST) IT!>>

CSS

Cascading Style Sheets, or CSS, are a way to set how something appears on a web page. This wiki allows you to apply predefined CSS classes to tables, table rows, table cells, and to spans of text and HTML blocks.

Applying CSS

If you are using MoinMoin markup (versus Creole markup - see Wiki Best Practices) CSS can be applied to tables or parts of them with these notations:

  • <class="..."> will put that CSS class into cell (td) html

  • <rowclass="..."> will put that CSS class into row (tr) html

  • <tableclass="..."> will put that class into table (table) html

  • <id="..."> will put that CSS id into cell (td) html

CSS can be applied to text spans and HTML blocks using the span and div macros (see above).

Predefined CSS Classes

This wiki does not allow you to specify arbitrary CSS styling in pages. You can, however, use any of these predefined CSS classes on pages:

Class

Description

Example

Effect

red, green, blue

Set the background to red, green, or blue.

This shows the <<span(red)>>red<<span>>, <<span(green)>>green<<span>>, and <<span(blue)>>blue<<span>> classes.

This shows the red, green, and blue classes.

th

Specify that a table row or table cell is a table header ("th" in HTML).

||<rowclass="th"> Class || Description || Example ...

See top of this table.

solid, dashed, dotted

Create a border around an HTML block that is solid, dashed or dotted.

<<div(solid)>>A solid border<<div>>
<<div(dashed)>>A dashed border<<div>>
<<div(dotted)>>A dotted border<<div>>

A solid border
A dashed border
A dotted border

center

Center the text in an HTML block in the middle of the page/enclosing block.

<<div(center)>>Centered!<<div>>
Not in the center at all.

Centered!
Not in the center at all.

right

Float an HTML block to the right side of the page.

<<div(right)>><<div(solid)>>I'm right!<<div>><<div>> A bit of text to demonstrate what a floating right block looks like. This also shows nested calls to the div macro.

I'm right!
A bit of text to demonstrate what a floating right block looks like. This also shows nested calls to the div macro.

title

Used at top of a page to display a title string on it. Titles are slightly larger than "=" section headers, and do not appear in the Table of Contents for the page.

<<div(title)>>Wiki Help<<div>>

Wiki Help

indent

Indent a section

Unindented.
<<div(indent)>>Indented<<div>>

Unindented.

Indented

Other CSS classes can be defined. If you want something please send a request to Galaxy Outreach.

InterWiki

This wiki supports InterWiki links. In addition to the standard InterWiki links that come with MoinMoin, we have added a few:

devthread:

Links to a post in the Galaxy-Dev mailing list archive

userthread:

Links to a post in the Galaxy-User mailing list archive

announcethread:

Links to a post in the Galaxy-Announce mailing list archive

francethread:

Links to a post in the Galaxy-France mailing list archive

srcdoccentral:

Links to source code documentation for the Galaxy development branch at ReadTheDocs

srcdocdist:

Links to source code documentation for the latest Galaxy release at ReadTheDocs

main:

Link to Main's landing page.

Data_Libraries:

| Link to Main's Data Library list.

Published_Histories:

| Link to Main's Published Histories list

Published_Workflows:

| Link to Main's Published Workflows list

Published_Visualizations:

| Link to Main's Published Visualizations list

Published_Pages:

| Link to Main's Published Pages list

Other

trello:

Link to the Galaxy Issues Trello board. Use the complete URL to link to a specific card on that board.

toolshedview:

Link to a page in the Galaxy Tool Shed, usually a repository

pmid:1234567

Links to the PubMed page for the given ID.

gmod:

Links to a page at the GMOD wiki

Best Practices

This wiki has best practices.

Theme

This wiki uses a modified version of the Mandarin theme. The structural elements are largely the same, but many details like colors and fonts have been modified.