addition plugin for frozen #4

_config.yml

@@ -68,4 +68,4 @@ kramdown:
   hard_wrap:     false
   footnote_nr:   1
   show_warnings: true
-  parse_block_html: true
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+ # parse_block_html: true
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_layouts/frozen.html

@@ -7,7 +7,7 @@
   <div class="main">
     <div class="content-wrapper">
       {%- include header.html -%}
-      <main class="fpage-content" aria-label="Content">
+      <main class="page-content" aria-label="Content">
         <div class="wrapper">
           {{ content }}
         </div>

_plugins/manual-markdown.rb

+def render(context)
+  site = context.registers[:site]
+  converter = site.find_converter_instance(::Jekyll::Converters::Markdown)
+  content = converter.convert(super)
+
+  output = <<~EOS
+<div>
+  #{content}
+</div>
+  EOS
+
+  output
+end
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_plugins/rblock.rb

+module Jekyll
+    module Tags
+      class RblockTag < Liquid::Block
+        def initialize(tag_name, block_options, liquid_options)
+            super
+            @title = block_options.strip
+        end
+  
+        def render(context)
+            rgridblockID = context["rgridblockID"]
+           
+            #content = super
+            site = context.registers[:site]
+            converter = site.find_converter_instance(::Jekyll::Converters::Markdown)
+            content = converter.convert(super)
+         
+
+       
+            #Because we’re not changing the context, there’s no need to push the context stack as with the rgridblock. 
+            # generate collapsible card HTML
+            output = <<~EOS
+<div class="rblock">
+    <h3>#{@title}</h3>
+    <hr>
+    <p>
+    #{content}
+    </p>
+</div>
+    EOS
+        
+            output
+        end
+      end
+    end
+  end
+  
+  Liquid::Template.register_tag('rblock', Jekyll::Tags::RblockTag)
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_plugins/rgridblock.rb

+module Jekyll
+    module Tags
+        class RgridblockTag < Liquid::Block
+            def initialize(tag_name, block_options, liquid_options)
+                super
+                @rgridblockID = "rgridblock-#{block_options.strip}"
+            end
+
+
+
+            def render(context)
+                #Pushes a new local scope on the stack, pops it at the end of the block
+                #Each new rgridblock  creates a new scope, and contexts have a custom implementation of [] to search up the stack for a matching value.
+                context.stack do
+                    context["rgridblockID"] = @rgridblockID
+                    @content = super
+                end
+                # The last bit we add is saving the resulting output of our block contents to an instance variable so we can access it outside of the stack scope.
+                output= %(<div class="rgridblock" id="#{@rgridblockID}">#{@content}</div>)
+                output
+              
+            end
+        end
+    end
+end
+
+Liquid::Template.register_tag('rgridblock', Jekyll::Tags::RgridblockTag)
+
+            
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_plugins/rtitle.rb

+module Jekyll
+    module Tags
+      class RtitleTag < Liquid::Block
+        def initialize(tag_name, block_options, liquid_options)
+            super
+            @title = block_options.strip
+        end
+  
+        def render(context)
+            site = context.registers[:site]
+            converter = site.find_converter_instance(::Jekyll::Converters::Markdown)
+            content = converter.convert(super)
+            output = <<~EOS
+<div class="rtitle">
+<h2>#{@title}</h2>
+    #{content}
+</div>
+    EOS
+        
+            output
+        end
+      end
+    end
+  end
+  
+Liquid::Template.register_tag('rtitle', Jekyll::Tags::RtitleTag)
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frozen.md

@@ -7,80 +7,29 @@ title: frozen
 order: 4
 ---
 
-{: .rtitle}
-<div>
-## IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
 
-Please cite the article on [Genome Biology][urlGenomeBiology].
-Shaman Narayanasamy†, Yohan Jarosz†, Emilie E. L. Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C. Laczny, Nicolás Pinel, Patrick May and Paul Wilmes*
-</div>
+{% rtitle Modeling Parkinson's disease in midbrain-like organoids %}
+Please cite the article on [NPJ Parkinson's disease](https://doi.org/10.1038/s41531-019-0078-4).
+Lisa M Smits†, Lydia Reinhardt†, Peter Reinhardt, Michael Glatza, Anna S Monzel, Nacny Stanslowsky, Marcelo D Rosato-Siri, Alessandra Zanon, Paul M Antony, Jessica Bellmann, Sarah M Nicklas, Kathrin Hemmer, Xiaobing Qing, Emanuel Berger, Norman Kalmbach, Marc Ehrlich, Silvia Bolognin, Andrew A Hicks, Florian Wegner, Jared L. Sterneckert* & Jens C Schwamborn*
+{% endrtitle %} 
 
-{: .rgridblock}
-<div>
-{: .rblock}
-<div>
-### <i class="fas fa-globe"></i> Website
-<hr>
-The **IMP** website hosted within *R3lab* frame is available [here][urlIMP].
-</div>
 
-{: .rblock}
-<div>
-### <i class="fas fa-code"></i> Source code
-<hr>
-The source code of IMP is available on the [LCSB Gitlab][urlGitIMP] where you can traceback what have been done by the authors.
-</div>
+{% rgridblock a-unique-id %}
+{% rblock Raw data %}
+The complete **Dataset** is available [here](https://webdav-r3lab.uni.lu/public/data/modeling-parkinsons-disease-in-midbrain-like-organoids/).
+{% endrblock %}
 
 
-{: .rblock}
-<div>
-### <i class="fas fa-code"></i> Additionnal source code
-<hr>
-Some additionnal analysis made on the paper as also available on the [LCSB Gitlab][urlGitIMPDoc].
-</div>
+{% rblock source code %}
+The source code used to make the publication is available on [Github](https://github.com/LCSB-DVB/Smits_Reinhardt_2019) where you can traceback what have been done by the authors.
+{% endrblock %}
 
-{: .rblock}
-<div>
-### <i class="fas fa-cogs"></i> Workflow
-<hr>
-Snakemake, a reproducible workflow engine that allow us IMP users execute the same workflow for each analysis. From [Köster, Johannes and Rahmann, Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.][urlBioinformatic]
-</div>
 
-{: .rblock}
-<div>
-### <i class="fas fa-dolly-flatbed"></i> Tool repository
-<hr>
-The **IMP** tool repository is hosted on the [LCSB webdav storage][urlWebdavIMP]. You will find some of the tools installed within IMP. IMP versions are stored under the dist folder.
-</div>
 
-{: .rblock}
-<div>
-### <i class="fab fa-docker"></i> Environment
-<hr>
-All tools dependencies of IMP are frozen inside a docker container. The files used to build the container can be found on Gitlab and versioned tarballs of the containers are found under the [webdav][urlWebdavIMPDep].
-</div>
+{% rblock microarray data %}
+Data is accessible through [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127967) website.
+{% endrblock %}
+{% endrgridblock %} 
 
-{: .rblock}
-<div>
-### <i class="fas fa-wrench"></i> R toolkit
-<hr>
-We use the [checkpoint][urlLibraryCheck] library to ensure that all of the necessary R packages are installed with the correct versions.
-</div>
 
-{: .rblock}
-<div>
-### <i class="fas fa-book"></i> Report
-<hr>
- **IMP** report contains all information needed to reproduce the same workflow, from the version of **IMP** used to make the analysis to the configuration file used to start the workflow. Everything is condensed and organized within an HTML report. Some reports can be found [here][urlIMPReport].
-</div>
-</div>
 
-[urlIMP]:https://imp.pages.uni.lu/web/
-[urlGenomeBiology]:https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1116-8
-[urlGitIMP]:https://git-r3lab.uni.lu/IMP/IMP
-[urlGitIMPDoc]:https://git-r3lab.uni.lu/IMP/IMP_manuscript_analysis
-[urlBioinformatic]:https://academic.oup.com/bioinformatics/article/28/19/2520/290322
-[urlWebdavIMP]:https://webdav-r3lab.uni.lu/public/R3lab/IMP/
-[urlWebdavIMPDep]:https://webdav-r3lab.uni.lu/public/R3lab/IMP/dist/
-[urlLibraryCheck]:https://cran.r-project.org/web/packages/checkpoint/vignettes/checkpoint.html
-[urlIMPReport]:https://webdav-r3lab.uni.lu/public/R3lab/IMP/reports/
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index.md

@@ -14,4 +14,6 @@ The theme is displayed via Gitlab [pages](https://core-services.pages.uni.lu/jek
 Read the [README](https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default/blob/master/README.md) file to know how to use in your project.
 
 
-To start a new page for your repository, you can fork [this project](https://git-r3lab.uni.lu/core-services/pages-jekyll-lcsb-template) and start to modify it directly.
\ No newline at end of file
+To start a new page for your repository, you can fork [this project](https://git-r3lab.uni.lu/core-services/pages-jekyll-lcsb-template) and start to modify it directly.
+
+