Menu
▾
▴
Re: [Gmod-tripal-devel] GBrowse, JBrowse and Tripal integration
|
From: Stephen F. <spf...@gm...> - 2013-10-14 16:00:47
|
Hi Scott, Would you like for GBrowse or JBrowse to automatically show the feature and all alignments, something like this page: http://www.rosaceae.org/prunus/prunus_persica/ppa000475m?block=alignments But, rather than just an image, you would like the application visible in an iFrame with the feature automatically in view? I believe you may be able to do this with minimal coding using CCK elements. Tripal already uses CCK elements to allow for easy addition of new items to the Resources right-sidebar. Instructions for doing this are on the Tripal v1.1 tutorial: http://www.gmod.org/wiki/Tripal_Tutorial_v1.1#Adding_New_Resources_To_Pages. Unfortunately, I have never tried to add a bit of PHP code to the CCK field, which is what you'd need to do to be able to generate a URL for the iFrame for the specific feature shown on the page. I think it can be done and if you'd like to go this route I can try to help figure out how to do it. Second, you can do this by creating a custom template file. There are instructions on the Tripal Developer's Handbook (http://www.gmod.org/wiki/Tripal_Developer's_Handbook <http://www.gmod.org/wiki/Tripal_Developer%27s_Handbook>) for how to add new template files and using the Tripal API to get data. In short, here is what you'd do: 1) Copy all of the templates from the Tripal theme into your default theme directory. This way, when Tripal is updated your custom templates won't be overwritten 2) In the tripal_theme/tripal_feature directory, add a new subtemplate file for your iframe content. 3) Add an 'include' statement in the node-chado_feature.tpl.php file to include your new subtemplate file 4) Add code to your subtepmlate file for creating the iFrame with the proper URL for displaying the feature. Once you get used to how the templates work, it is very easy to add new templates, and the Tripal API makes it relatively easy to get data. You shouldn't have to do any SQL queries at all in the template files. I can provide more specific details depending on how you want to go with this. Hope this helps, Stephen On 10/11/2013 12:46 PM, Scott Cain wrote: > Hi Stephen and all, > > I'm looking a way to put GBrowse and JBrowse iframes in feature pages, > presumably as separate tabs (added to the list of resources things > that would go along with relationships, annotated sequence, etc). I > would like to do this for the GMOD in the Cloud/Box and would like for > it to remain usable from one point release to the next. I'm guessing > there is documentation on how to do something like this; could you > please point it out for me? > > Also, I want to make links in GBrowse and JBrowse that go to the > feature pages in Tripal. Are the URLs always like > lowercase(genus/genus_species/uniquename)? > > Thanks, > Scott > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk > > > _______________________________________________ > Gmod-tripal-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel |
