Commit 9fdb35a7 authored by Elisabeth Guerard's avatar Elisabeth Guerard
Browse files

addition plugin for frozen #4

parent bf6b99e5
......@@ -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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......@@ -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>
......
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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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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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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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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......@@ -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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......@@ -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.
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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.
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