Commit 246fff18 authored by Yohan Jarosz's avatar Yohan Jarosz
Browse files

add frozen

parent 2cb76115
......@@ -40,3 +40,14 @@ plugins:
# - vendor/cache/
# - vendor/gems/
# - vendor/ruby/
kramdown:
auto_ids: true
entity_output: as_char
toc_levels: 1..6
smart_quotes: lsquo,rsquo,ldquo,rdquo
input: GFM
hard_wrap: false
footnote_nr: 1
show_warnings: true
parse_block_html: true
\ No newline at end of file
<!DOCTYPE html>
<html lang="{{ page.lang | default: site.lang | default: "en" }}">
{%- include head.html -%}
<body>
<div class="main">
{%- include header.html -%}
<main class="page-content" aria-label="Content">
<div class="wrapper">
{{ content }}
</div>
</main>
{%- include footer.html -%}
</div>
</body>
</html>
......@@ -21,7 +21,7 @@ $grey-color-dark: darken($grey-color, 25%) !default;
$table-text-align: left !default;
// Width of the content area
$content-width: 960px !default;
$content-width: 1080px !default;
$on-palm: 600px !default;
$on-laptop: 960px !default;
......@@ -50,5 +50,6 @@ $banner-height: 100px;
@import
"minima/base",
"minima/layout",
"minima/frozen",
"minima/syntax-highlighting"
;
......@@ -173,7 +173,7 @@ pre {
max-width: $content-width;
margin-right: auto;
margin-left: auto;
height: 100%;
min-height: 100%;
@extend %clearfix;
position: relative;
background-color: $background-color;
......
.rtitle {
margin: 0px 20px 50px 20px;
padding: 30px;
border: 1px solid darkgrey;
p {
color: #666666;
@include relative-font-size(0.9);
}
}
.rblock {
margin: 0px 20px 50px 20px;
padding: 10px 30px 10px 30px;
outline: 1px solid darkgrey;
height: 330px;
width: $content-width / 5 + 24;
float: left;
p {
color: #666666;
@include relative-font-size(0.9);
display: inline-block;
vertical-align: middle;
float: none;
text-align: justify;
padding-top: 30px;
}
}
hr {
border: 0;
height: 1px;
background-image: linear-gradient(to right, rgba(0, 0, 0, 0.20), rgba(0, 0, 0, 0.6), rgba(0, 0, 0, 0.2));
}
\ No newline at end of file
......@@ -109,7 +109,7 @@
*/
.site-footer {
padding: $spacing-unit 0;
position: absolute;
#position: absolute;
bottom: 0;
height: $spacing-unit * 2;
display:flex;
......
---
# You don't need to edit this file, it's empty on purpose.
# Edit theme's home layout instead if you wanna make some changes
# See: https://jekyllrb.com/docs/themes/#overriding-theme-defaults
layout: frozen
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.
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>
{: .rblock}
<div>
## Website
<hr>
The *IMP* website hosted within *R3lab* frame is available [here](href="http://r3lab.uni.lu/web/imp/index.html").
</div>
{: .rblock}
<div>
## 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.
</div>
{: .rblock}
<div>
## Additionnal source code
<hr>
Some additionnal analysis made on the paper as also available on the LCSB Gitlab.
</div>
{: .rblock}
<div>
## 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.
</div>
{: .rblock}
<div>
## 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.
</div>
{: .rblock}
<div>
## 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.
</div>
{: .rblock}
<div>
## R toolkit
<hr>
We use the checkpoint library to ensure that all of the necessary R packages are installed with the correct versions.
</div>
{: .rblock}
<div>
## 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>
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