Commit bf6b99e5 authored by Elisabeth Guerard's avatar Elisabeth Guerard
Browse files

finish frozen layout #22

parent cc74b9e9
......@@ -19,7 +19,6 @@ banner: default # When you have custom images, change this setting's value to t
# Refer to assets/banners/default or assets/banners/frozen
logo: small # Change to "big" (without quotas) in case of having broad logo
new_menu: false
date: "2018"
description: >- # this means to ignore newlines until "baseurl:"
This is a default LCSB Jekyll template.
baseurl: "/jekyll-theme-lcsb-default" # the subpath of your site, e.g. /blog
......
......@@ -8,34 +8,72 @@
padding-bottom: $footer-height;
}
.rtitle {
margin: 0px 20px 50px 20px;
.rtitle {
margin: 0px 20px 50px 0px;
padding: 30px;
border: 1px solid darkgrey;
h2 {
text-transform: uppercase;
font-size: 15px;
margin: 8px;
padding: 0px;
color:black;
}
p {
color: #666666;
@include relative-font-size(0.9);
padding-top: 30px;
}
}
.rgridblock {
display:grid;
grid-template-columns:repeat(3, 1fr);
}
@media only screen and (max-width: 768px) {
.rgridblock {
display: grid;
grid-template-columns: 1fr;
}
}
.rblock {
margin: 0px 20px 50px 20px;
padding: 10px 30px 10px 30px;
margin: 0px 20px 50px 0px;
padding: 10px 30px 10px 30px;
outline: 1px solid darkgrey;
height: 330px;
width: $content-width / 5 + 24;
float: left;
h3 {
font-size: 15px;
text-transform: uppercase;
color: black;
margin: 8px;
padding: 0px;
}
p {
color: #666666;
@include relative-font-size(0.9);
display: inline-block;
vertical-align: middle;
float: none;
text-align: justify;
text-align: left;
padding-top: 30px;
}
}
hr {
border: 0;
......
......@@ -7,70 +7,80 @@ 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.
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>
{: .rgridblock}
<div>
{: .rblock}
<div>
## <i class="fas fa-globe"></i> Website
### <i class="fas fa-globe"></i> Website
<hr>
The *IMP* website hosted within *R3lab* frame is available [here](href="http://r3lab.uni.lu/web/imp/index.html").
The **IMP** website hosted within *R3lab* frame is available [here][urlIMP].
</div>
{: .rblock}
<div>
## <i class="fas fa-copy"></i> Source code
### <i class="fas fa-code"></i> Source code
<hr>
The source code of IMP is available on the LCSB Gitlab where you can traceback what have been done by the authors.
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}
<div>
## <i class="fas fa-copy"></i> Additionnal source code
### <i class="fas fa-code"></i> Additionnal source code
<hr>
Some additionnal analysis made on the paper as also available on the LCSB Gitlab.
Some additionnal analysis made on the paper as also available on the [LCSB Gitlab][urlGitIMPDoc].
</div>
{: .rblock}
<div>
## <i class="fas fa-cogs"></i> Workflow
### <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.
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
### <i class="fas fa-dolly-flatbed"></i> Tool repository
<hr>
The IMP tool repository is hosted on the LCSB webdav storage. You will find some of the tools installed within IMP. IMP versions are stored under the dist folder.
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
### <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.
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
### <i class="fas fa-wrench"></i> R toolkit
<hr>
We use the checkpoint library to ensure that all of the necessary R packages are installed with the correct versions.
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
### <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.
</div>
\ No newline at end of file
**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
......@@ -2,7 +2,7 @@
Gem::Specification.new do |spec|
spec.name = "jekyll-theme-lcsb-default"
spec.version = "0.2.20"
spec.version = "0.2.21"
spec.authors = ["Trefex", "jaceklebioda_lux"]
spec.email = ["lcsb-sysadmins@uni.lu"]
......@@ -15,6 +15,8 @@ Gem::Specification.new do |spec|
spec.add_runtime_dependency "jekyll", "~> 3.8"
spec.add_runtime_dependency "jekyll-seo-tag", "~> 2.5"
spec.add_development_dependency "bundler", "~> 1.16"
spec.add_development_dependency "bundler", ">= 1.16.1"
spec.add_development_dependency "rake", "~> 12.3"
end
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