From: Dan B. <dan...@gm...> - 2011-04-21 00:46:52
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Sorry for cross posting, hopefully these lists are largely orthogonal, At some point I remember seeing a demonstration of a GBrowse embedded within a MediaWiki page. Can anyone point me at that work? Unfortunately, this search http://goo.gl/kZXoU doesn't turn up anything :-/ Cheers, Dan. |
From: Jason S. <jas...@gm...> - 2011-04-21 01:51:28
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http://ecoliwiki.net/colipedia/index.php/lacZ:Gene On Apr 20, 2011, at 5:46 PM, Dan Bolser wrote: > Sorry for cross posting, hopefully these lists are largely orthogonal, > > At some point I remember seeing a demonstration of a GBrowse embedded > within a MediaWiki page. Can anyone point me at that work? > Unfortunately, this search http://goo.gl/kZXoU doesn't turn up > anything :-/ > > > Cheers, > Dan. > > ------------------------------------------------------------------------------ > Benefiting from Server Virtualization: Beyond Initial Workload > Consolidation -- Increasing the use of server virtualization is a top > priority.Virtualization can reduce costs, simplify management, and improve > application availability and disaster protection. Learn more about boosting > the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
From: Daniel R. <dan...@gm...> - 2011-04-21 05:29:35
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Dan, Last year I wrote a MediaWiki extension for EcoliWiki that does just that: creates an image from gbrowse in a wiki page. Essentially it is a PHP wrapper for the gbrowse_img script that comes packaged with gbrowse. ( gbrowse_img documentation at EcoliWiki <http://trimer.tamu.edu/cgi-bin/gbrowse_img> ) Attached is the gbrowse_img.php script. This extension requires that the Mediawiki setting $wgAllowExternalImages<http://www.mediawiki.org/wiki/Manual:$wgAllowExternalImages>be turned on. In LocalSettings.php you can add: # Allow linking images (hot-linking) $wgAllowExternalImages = true; Then you can display an image by putting an HTML-like tag in the wikitext of a page. Most (if not all) of the parameters are named the same thing in gbrowse_img (for consistency.) The parameters are simple key=value pairs within the <tags>. See the script for all the available parameters. Example: <gbrowseImage> name=NC_010473:430647..432578 source=ecoli_DH10B preset=GeneLocation </gbrowseImage> Also, a word about the script: there are some constants set (around lines 54-63) that will need changing. At EcoliWiki we wanted to show +/-1000bp on either side of the gene/feature, this is set by the PADDING_LENGTH constant. It can be set to 0. There are two other constants that need changing...URLs to gbrowse and gbrowse_img, respectively. I have added a section (lines ~224-333) for creating presets (sets of options that always go together.) If anyone is interested or wants more information feel free to email me off-list. -Daniel http://ecoliwiki.net/User:DanielRenfro Hu Lab Research Associate 979-862-4055 On Wed, Apr 20, 2011 at 7:46 PM, Dan Bolser <dan...@gm...> wrote: > Sorry for cross posting, hopefully these lists are largely orthogonal, > > At some point I remember seeing a demonstration of a GBrowse embedded > within a MediaWiki page. Can anyone point me at that work? > Unfortunately, this search http://goo.gl/kZXoU doesn't turn up > anything :-/ > > > Cheers, > Dan. > > -- > BioWiki mailing list: > bio...@go... > > Subscription & archives: > http://groups.google.com/group/biowiki-l > > Unsubscribe: > bio...@go... > |