Tuesday, July 16, 2013

Digital lab book using pmwiki on isbrae

So, documentation is of course very important.  In our work, we don't always have a lab book, as much of our stuff happens at the computer....

But we can use that computer for logging what we do- it's really useful.  To that end, I've copied Dan Breton's workflow using pmwiki, an open source package for making wiki pages.  This makes it pretty straightforward to just use the web page for a notebook.  

To get yourself started with pmwiki on isbrae:

First you need an account.  Once you've done that, you should have a public_html folder under your home directory:

[bo@isbrae public_html]$ pwd
[bo@isbrae public_html]$ 

If you haven't already got one, make that first.  Then, copy the wiki-skeleton set of files that Dan set up in his public_html directory:

[bo@isbrae ~]$ cp -r /home/dbreton/public_html/wiki_skeleton ~/public_html/hawley_wiki

(substitute your favorite name for 'hawley_wiki' above)

Now, you need to momentarily make a quick opening for pmwiki to access the directory, so exectute

[bo@isbrae public_html]$ chmod 2777 hawley_wiki/

And then open your favorite browser on your desktop/laptop/whatever computer and navigate to:


(where you replace <username> and <wiki_name> with your username and the wikiname you chose earlier, respectively).

Now that pmwiki has been initialized, you can close up the permissions again:

[bo@isbrae public_html]$ chmod 755 hawley_wiki/

Your wiki page is now active on the link to which you just navigated.  

And then you can start wiki'ing!  See Dan's wiki at http://isbrae.dartmouth.edu/pmwiki/pmwiki.php for more documentation on how to work with pmwiki and the special things Dan's set up to help make our lives easier.  Also see the pmwiki site and all the support pages.  It's not that hard once you get it up and running!

Hope this helps!

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