Commit d2222209 authored by Elisabeth Guerard's avatar Elisabeth Guerard
Browse files

reformat frozen page to use liquid tag rtitle / rblock / ..#2

parent cd79a887
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......@@ -2,4 +2,3 @@ _site
.sass-cache
.jekyll-metadata
Gemfile.lock
/_plugins
\ No newline at end of file
......@@ -5,81 +5,45 @@ title: Imp
permalink: /frozen/imp
---
{: .rtitle}
<div>
## IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Please cite the article on [Genome Biology][urlGenomeBiology].
{% rtitle IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses %}
Please cite the article on [Genome Biology](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1116-8).
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>
{% endrtitle %}
{% rgridblock a-unique-id %}
{% rblock Website | fas fa-globe %}
The **IMP** website hosted within *R3lab* frame is available [here](https://imp.pages.uni.lu/web/).
{% endrblock %}
{% rblock Source code | fas fa-code %}
The source code of IMP is available on the [LCSB Gitlab](https://git-r3lab.uni.lu/IMP/IMP) where you can traceback what have been done by the authors.
{% endrblock %}
{: .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 Additionnal source code | fas fa-code %}
Some additionnal analysis made on the paper as also available on the [LCSB Gitlab](https://git-r3lab.uni.lu/IMP/IMP_manuscript_analysis).
{% endrblock %}
{: .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>
{% rblock Workflow | fas fa-cogs %}
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.](https://academic.oup.com/bioinformatics/article/28/19/2520/290322)
{% 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 Tool repository | fas fa-dolly-flatbed %}
The **IMP** tool repository is hosted on the [LCSB webdav storage](https://webdav-r3lab.uni.lu/public/R3lab/IMP/). You will find some of the tools installed within IMP. IMP versions are stored under the dist folder.
{% 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 Environment | fab fa-docker %}
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](https://webdav-r3lab.uni.lu/public/R3lab/IMP/dist/).
{% endrblock %}
{: .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}
<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 R toolkit | fas fa-wrench %}
We use the [checkpoint](https://cran.r-project.org/web/packages/checkpoint/vignettes/checkpoint.html) library to ensure that all of the necessary R packages are installed with the correct versions.
{% endrblock %}
{: .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/
\ No newline at end of file
{% rblock Report | fas fa-book %}
**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](https://webdav-r3lab.uni.lu/public/R3lab/IMP/reports/).
{% endrblock %}
{% endrgridblock %}
......@@ -5,41 +5,25 @@ title: Imp
permalink: /frozen/modelingParkinson
---
{: .rtitle}
<div>
## Modeling Parkinson's disease in midbrain-like organoids
Please cite the article on [NPJ Parkinson's disease][urlDoi].
{% 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 %}
</div>
{: .rgridblock}
<div>
{: .rblock}
<div>
### <i class="fas fa-file-download"></i> RAW DATA
<hr>
The complete **Dataset** is available [here][urlWebdav].
</div>
{: .rblock}
<div>
### <i class="fas fa-code"></i> Source code
<hr>
The source code used to make the publication is available on [Github][urlGithub] where you can traceback what have been done by the authors.
</div>
{: .rblock}
<div>
### <i class="fas fa-globe"></i> Microarray data
<hr>
Data is accessible through [NCBI GEO][urlNCBI] website.
</div>
</div>
[urlDoi]:https://doi.org/10.1038/s41531-019-0078-4
[urlWebdav]:https://webdav-r3lab.uni.lu/public/data/modeling-parkinsons-disease-in-midbrain-like-organoids/
[urlGithub]:https://github.com/LCSB-DVB/Smits_Reinhardt_2019
[urlNCBI]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127967
\ No newline at end of file
{% rgridblock a-unique-id %}
{% rblock Raw data | fas fa-file-download %}
The complete **Dataset** is available [here](https://webdav-r3lab.uni.lu/public/data/modeling-parkinsons-disease-in-midbrain-like-organoids/).
{% endrblock %}
{% 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 microarray data | fas fa-globe %}
Data is accessible through [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127967) website.
{% endrblock %}
{% endrgridblock %}
......@@ -5,39 +5,23 @@ title: Imp
permalink: /frozen/singlecell
---
{: .rtitle}
<div>
## SINGLE-CELL TRANSCRIPTOMICS REVEALS MULTIPLE NEURONAL CELL TYPES IN HUMAN MIDBRAIN-SPECIFIC ORGANOIDS
Please cite the article on [BioRxiv][urlBioRxiv].
Lisa M Smits†, Magni Stefano, Grzyb Kamil, Antony Paul MA, Krüger Rejko, Skupin Alexander, Bolognin Silvia, Jens C Schwamborn*
</div>
{: .rgridblock}
<div>
{: .rblock}
<div>
### <i class="fas fa-code"></i> SOURCE CODE
<hr>
The complete **Dataset** is available [here][urlWebdav].
</div>
{% rtitle SINGLE-CELL TRANSCRIPTOMICS REVEALS MULTIPLE NEURONAL CELL TYPES IN HUMAN MIDBRAIN-SPECIFIC ORGANOIDS %}
Please cite the article on [BioRxiv](https://www.biorxiv.org/content/10.1101/589598v1).
Lisa M Smits†, Magni Stefano, Grzyb Kamil, Antony Paul MA, Krüger Rejko, Skupin Alexander, Bolognin Silvia, Jens C Schwamborn*
{% endrtitle %}
{: .rblock}
<div>
### <i class="fas fa-file-download"></i> SINGLE-CELL TRANSCRIPTOMICS
<hr>
Data is accessible through [LCSB WebDAV][urlWebdav] website.
</div>
{% rgridblock a-unique-id %}
{% rblock SOURCE CODE | fas fa-code %}
The complete **Dataset** is available [here](https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/single-cell_transcriptomics/).
{% endrblock %}
{: .rblock}
<div>
### <i class="fas fa-file-download"></i> RAW DATA
<hr>
The complete Dataset is available [here][urlWebdavall].
</div>
</div>
{% rblock SINGLE-CELL TRANSCRIPTOMICS | fas fa-file-download %}
Data is accessible through [LCSB WebDAV](https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/single-cell_transcriptomics/) website.
{% endrblock %}
[urlBioRxiv]:https://www.biorxiv.org/content/10.1101/589598v1
[urlWebdavall]: https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/raw-data/
[urlWebdav]:https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/single-cell_transcriptomics/
\ No newline at end of file
{% rblock RAW DATA | fas fa-file-download %}
The complete Dataset is available [here](https://webdav-r3lab.uni.lu/public/data/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids/raw-data/).
{% endrblock %}
{% endrgridblock %}
......@@ -5,47 +5,35 @@ title: Smartr
permalink: /frozen/smartr
---
{: .rtitle}
<div>
## SmartR: An open-source platform for interactive visual analytics for translational research data
<hr>
Please cite the article on [Oxford Bioinformatics][urlDoi].
{% rtitle SmartR: An open-source platform for interactive visual analytics for translational research data %}
Please cite the article on [Oxford Bioinformatics](https://doi.org/10.1093/bioinformatics/btx137).
Sascha Herzinger, Wei Gu, Venkata Satagopam, Serge Eifes, Kavita Rege, Adriano Barbosa-Silva, Reinhard Schneider, on behalf of the eTRIKS Consortium
</div>
{: .rgridblock}
<div>
{: .rblock}
<div>
### <i class="fas fa-globe"></i> Website
<hr>
The **SmartR** website hosted by **R3lab** is available [here][urlSmartR].
</div>
{: .rblock}
<div>
### <i class="fas fa-code"></i> Source code
<hr>
The source code of SmartR is available on [GitHub][urlSourceSmartR].
</div>
{: .rblock}
<div>
### <i class="fas fa-book"></i> Documentation
<hr>
All available documentation can be found [here][urlDocSmartR]
</div>
{: .rblock}
<div>
### <i class="fas fa-video"></i> Videos
<hr>
Several videos have been recorded to showcase the capabilities of SmartR. They can be accessed via [YouTube][urlYouTubeSmartR].
</div>
</div>
[urlYouTubeSmartR]: https://www.youtube.com/channel/UC0LP15lmuMkgYYLaFj3SKew
[urlDocSmartR]: https://github.com/transmart/SmartR/tree/master/doc
[urlSourceSmartR]:https://github.com/transmart/SmartR
[urlSmartR]: http://smartr.lcsb.uni.lu/
[urlDoi]: https://doi.org/10.1093/bioinformatics/btx137
{% endrtitle %}
{% rgridblock a-unique-id %}
{% rblock Website | fas fa-globe %}
The **SmartR** website hosted by **R3lab** is available [here](http://smartr.lcsb.uni.lu/).
{% endrblock %}
{% rblock Source code | fas fa-code %}
The source code of SmartR is available on [GitHub](https://github.com/transmart/SmartR).
{% endrblock %}
{% rblock Documentation | fas fa-book %}
All available documentation can be found [here](https://github.com/transmart/SmartR/tree/master/doc)
{% endrblock %}
{% rblock Videos | fas fa-video %}
Several videos have been recorded to showcase the capabilities of SmartR. They can be accessed via [YouTube](https://www.youtube.com/channel/UC0LP15lmuMkgYYLaFj3SKew).
{% endrblock %}
{% endrgridblock %}
......@@ -32,8 +32,8 @@ linkedin_schoolname: university-of-luxembourg
# Build settings
markdown: kramdown
kramdown:
parse_block_html: true
#kramdown:
#parse_block_html: true
theme: jekyll-theme-lcsb-default
plugins:
- jekyll-feed
......
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
\ No newline at end of file
module Jekyll
module Tags
class RblockTag < Liquid::Block
def split_params(params)
params.split("|").map(&:strip)
end
def initialize(tag_name, block_options, liquid_options)
super
args = split_params(block_options)
@title = args[0]
if args.length >1
@icon = args[1]
else
#default icon
@icon = "fas fa-code"
end
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>
<i class="#{@icon}"></i>
#{@title}
</h3>
<hr>
<p>
#{content}
</p>
</div>
EOS
output
end
end
end
end
Liquid::Template.register_tag('rblock', Jekyll::Tags::RblockTag)
\ No newline at end of file
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)
\ No newline at end of file
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>
<hr>
#{content}
</div>
EOS
output
end
end
end
end
Liquid::Template.register_tag('rtitle', Jekyll::Tags::RtitleTag)
\ No newline at end of file
......@@ -10,14 +10,14 @@ Here you can find a collection of tools used @LCSB to provide support for reprod
## Associated services
[![Gitlab]({{ "//images/gitlab-logo.png" | relative_url }}){:width="120px"}](https://git-r3lab.uni.lu/)
[![Gitlab]({{ "//images/gitlab-logo.png" | relative_url }}){:width="120px"}](https://git-r3lab.uni.lu/){:target="_blank"}
**Gitlab** is an open source software that provide Version control and many other usefule features for devellopers and scientists.
[![Docker]({{ "//images/docker-logo.png" | relative_url }}){:width="120px"}](https://docker-r3lab.uni.lu)
[![Docker]({{ "//images/docker-logo.png" | relative_url }}){:width="120px"}](https://docker-r3lab.uni.lu){:target="_blank"}
**DOCKER** is an open source solution that allow us to package and freeze an application or framework and all it's dependencies into a single unit called a container.
[![Webdav]({{ "//images/webdav-logo.png" | relative_url }}){:width="120px"}](https://webdav-r3lab.uni.lu/)
[![Webdav]({{ "//images/webdav-logo.png" | relative_url }}){:width="120px"}](https://webdav-r3lab.uni.lu/){:target="_blank"}
**WEBDAV** is a file sharing system over the web that brings more advanced security and control that a traditionnal FTP server.
......
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