Galaxy Wiki
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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:
The default MoinMoin formatting syntax. How to make your text bold, italicized and many other things.
The details of Creole formatting syntax. This is an alternative to the MoinMoin "wiki" syntax. See also the nwwl Macro. You will need it. Pages can be either MoinMoin wiki or Creole, but not both.
Other help for users beyond just the syntax. how to edit a page, images, creating a new page, setting your preferences, and much more.
A thorough introduction to MoinMoin
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:
- Attach them to the page that links to them.
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]] |
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]] |
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 |
Applies a predefined CSS class (see CSS below) to a span of text. Care must be taken not to cross HTML blocks. |
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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. |
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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 ... |
Set 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>> |
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>> |
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! |
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. |
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:
Mailing List Links
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 |
Source Code Links
src: |
Links to a source file at Bitbucket |
codedoccentral: |
Links to source code documentation for the Galaxy development branch at ReadTheDocs |
codedocdist: |
Links to source code documentation for the latest Galaxy release at ReadTheDocs |
Links to Main
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 trello:Galaxy Issues Trello board. Use the complete URL to link to a specific card on that board. |
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.