Installing DokuWiki

Installing DokuWiki requires a webserver and access to the underlying operating system as an administrator. Once having setup the ELN, there should be no need any further to access the file system, as anything should be controllable via the DokuWiki web interface. However, during installation a few things can only be done with direct access to the file system that require basic familiarity with the command line and web servers.

This section will provide some advice with installing the DokuWiki base and the required plugins. Creating the first content and organising your wiki will be covered in the following sections. As installing the DokuWiki requires access on the operating-system level, you may seek help from your IT department or skilled colleagues for this part. This is particularly true for the base installation and the special configurations requiring files to be copied on the file system.

Base wiki

For general instructions of how to install DokuWiki, see the official installation instructions available online. Generally, system requirements of the DokuWiki are quite low, only a webserver and PHP are necessary. Basic configuration of the freshly installed DokuWiki is done using a web interface. Usually, you will want to set the wiki as a “closed wiki”, with every access requiring a user account.

After having installed a bare DokuWiki, you need to add a number of plugins. This can be done from the DokuWiki admin interface via a web browser or from the command line with file system access to the server. The latter is only suggested for experienced users or if you intend to automate the installation. For details, see the respective section of the official DokuWiki manual available online.

For a complete list of plugins that should be installed and a short description of their use within the ELN, see Table 1

Table 1 DokuWiki plugins necessary for using the wiki as ELN. The plugin names are given as specified in the official DokuWiki documentation available online, hence the inconsistent spelling/captalisation. Each plugin can be found by the given name and installed via the plugin manager available from the DokuWiki admin interface.

Name	Description
Bureaucracy	Web forms used to create pages, e.g., for the lab notebook and the inventory (samples, batches)
Structured Data / data	Collecting and storing structured data (metadata) on individual wiki pages; allows to aggregate information in overview tables and lists with filters (by Andreas Gohr)
sqlite	Interface to an SQLite database used solely for easier access to the data collected using the Structured Data plugin and contained in individual wiki pages (by Andreas Gohr)
templatepagename	Access to template files from within the wiki interface using special (and configurable) names
Definition List	Used for the protocol on the individual lab notebook pages providing a detailed list of tasks carried out prefixed with timestamps
caption	Figure and table captions, including referencing these captions
Wrap	Structure a wiki page, e.g., multiple columns and button-like areas
Icons	Include fontawesome and other icons into wiki pages, helpful for easier navigation and overview
confmanager	Access to the configuration files from within the DokuWiki admin area (by cosmo code)
folded	Create folded parts of a page, e.g., for help texts
include	Include other pages into a wiki page; used for help texts in conjunction with the folded plugin
Note	Simple way to add highlighted notes to wiki pages
tplinc	Conditionally include pages at certain parts of the DokuWiki template; useful, e.g., for area-specific additional navigation in the sidebar
upgrade	Upgrade the DokuWiki from within the admin interface (installed by default)
snippets	Insert templates into the current page at the cursor position helpful for more consistent documentation, reusing well-crafted building blocks
(bibtex)	not available via extension manager, needs rewrite and renaming

General configuration

There is a series of general configuration settings that should be changed from their defaults. This again can be done using the DokuWiki admin interface via a web browser. For details of the configuration settings to be changed and their respective values, see Table 2.

Table 2 Configuration settings of a DokuWiki installation used as ELN. The configuration is grouped into dokuwiki-specific and plugin-specific sections, and the former into separate blocks. Each configuration setting has a unique key that is given in small print on the configuration page. check and uncheck refer to checkboxes and their respective state.

Block	Key	Setting
DokuWiki
Basic	start	index
	dmode	0750
	fmode	0640
Display	breadcrumbs	0
	youarehere	check
	toptoclevel	2
	useheading	Wiki Content Only
Advanced	userewrite	.htaccess
	useslash	check
Plugins
Data	edit_content_only	check
Include	showfooter	uncheck
	showdate	uncheck
	showuser	uncheck
	showcomments	uncheck
	showlinkbacks	uncheck
	showtags	uncheck
	showeditbtn	uncheck
Snippets	snips_updatable	uncheck
	old_revisions	uncheck
	userreplace	uncheck

Of course, you can deviate from some of the settings given here without impairing functionality, as some are merely a matter of personal taste. Nevertheless, others are necessary for the DokuWiki to work as intended.

The start, userewrite, and useslash settings ensure the DokuWiki URLs to behave like ordinary URLs, given the appropriate configuration of your webserver, including rewrite rules.

breadcrumbs, youarehere, toptoclevel, and useheading are mainly a matter of taste, whereas the last configuration setting is crucial to have sensible information in the aggregation tables for labbook pages.

The edit_content_only setting of the Structured Data Plugin should be enabled, as otherwise, users editing the data tables will always be confronted with a rather complex form that allows for both, editing the values of the respective fields as well as their types. The latter, however, is neither necessary nor helpful to ensure consistency throughout your ELN.

Special configurations

The tplinc plugin needs some special attention, as by default, the standard template provided by DokuWiki does not support the include hooks. Therefore, according to the documentation of the tplinc plugin available online, you need to copy the configuration provided by the plugin to the global configuration file directory. Assuming a unixoid-like operating system, you would issue the following command from within the DokuWiki root directory:

cp lib/plugins/tplinc/dokuwiki/* conf/

Once done, in the special admin section for the tplinc plugin, you can include wiki pages at specific places of the template. Within the ELN, this is used as area-specific additional navigation in the sidebar.

Nice-to-have plugins

There are more plugins, that are nice to have as they offer additional functionality. Those can be found in table Table 3.

Table 3 Additional plugins for the DokuWiki-ELN which are handy and offer additional functionality. Each plugin can be found by the given name and installed via the plugin manager available from the DokuWiki admin interface.

Name	Description
searchindex	The searchindex can be completely rebuilt which is helpful after moving namespaces or adding pages via the file system. It is therefore most helpful during development.
todo	Creating To-do lists with checkmarks and saving who checked the mark when.
dw2pdf	Allows to download single pages or entire namespaces via URL extension. The pages created contain links the same as the original website. This format is therefore useful to exchange the contents of the labbook.
pdfjs	Embed pdf pages on wiki pages.