Commit 0097a34e authored by Maharshi Vyas's avatar Maharshi Vyas
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layout: default
order: -1
title: Imp
permalink: /Frozen/imp
Test IMP
layout: default
order: -1
title: Smartr
permalink: /Frozen/smartr
Test Frozen
......@@ -17,9 +17,11 @@ GEM
em-websocket (0.5.1)
eventmachine (>= 0.12.9)
http_parser.rb (~> 0.6.0)
eventmachine (1.2.7)
eventmachine (1.2.7-x64-mingw32)
faraday (0.15.3)
multipart-post (>= 1.2, < 3)
ffi (1.9.25)
ffi (1.9.25-x64-mingw32)
forwardable-extended (2.6.0)
http_parser.rb (0.6.0)
......@@ -91,13 +93,13 @@ GEM
thread_safe (~> 0.1)
tzinfo-data (1.2018.5)
tzinfo (>= 1.0.0)
wdm (0.1.1)
bundler (~> 1.16.1)
bundler (> 1.16.1)
jekyll (~> 3.7.3)
jekyll-feed (~> 0.6)
jekyll-paginate-v2 (~> 1.7)
......@@ -105,7 +107,6 @@ DEPENDENCIES
jekyll-theme-primer (~> 0.5.2)
minima (~> 2.0)
wdm (~> 0.1.0)
layout: default
title: Webistes
order: 3
permalink: /websites
Websites hosted within the R3lab frame.
TGM pipeline a platform for visually-aided exploration, analysis and interpretation of high-throughput translational medicine data
[IMP Integrated Meta-omic Pipeline]({{ "frozen/imp" | relative_url }})
[MINERVA a platform for Molecular Interaction NEtwoRk VisuAlization](
SYSCID Data Management Plan Information Collection
CaSiAn CaSiAn Website
......@@ -13,13 +13,13 @@
# you will see them accessed via {{ site.title }}, {{ }}, and so on.
# You can create any custom variable you would like, and they will be accessible
# in the templates via {{ site.myvariable }}.
title: Blank template using LCSB theme.
title: R3.
description: >- # this means to ignore newlines until "baseurl:"
Write an awesome description for your new site here. You can edit this
line in _config.yml. It will appear in your document head meta (for
Google search results) and in your feed.xml site description.
baseurl: "/pages-jekyll-lcsb-template" # the subpath of your site, e.g. /blog
baseurl: "/r3-pages" # the subpath of your site, e.g. /blog
url: "" # the base hostname & protocol for your site, e.g.
banner: default # When you have custom images, change this setting's value to the name of the folder containing them
layout: page
title: About
permalink: /about/
order: 2
This is the LCSB Jekyll theme. You can find out more info about customizing your Jekyll theme, as well as basic Jekyll usage documentation at [](
You can find the source code for this them at Gitlab:
We have successfully helped in publishing the following websites:
* [Page of theme](
* [This very page](
* [Minerva doc's](
* [PDmap blog](
* [IMP](
\ No newline at end of file
layout: default
title: Frozen Pages
order: 2
permalink: /frozen
Here you can find project pages that are related to a published scientific paper. Project pages must link to all components referenced in the paper and is not modified after the release of the paper.
This website is under version control on the [LCSB Gitlab](
layout: page
title: Help
permalink: /the-help/
order: 3
If you need help, don't hesitate to send us an email.
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......@@ -5,54 +5,7 @@
layout: default
title: Index
order: 1
permalink: /index
# Gitlab pages
Welcome to an example page!
Below you will find a detailed instruction on how to set-up your own gitlab website.
Sources for this page are [available in Gitlab](
Additionally, you can also navigate to the [repository for theme](
# Setting up your web page
## The process
0. Make sure that you have access to [gitlab]( If you ever cloned a repository or set-up a new one there, then you should be fine.
1. [Create an empty repository in gitlab]( Please bear in mind, that the both names of the namespace and the project influence
final address of the page - it will follow the `https://<namespace><project_name>` convention.
2. Clone this very repository: `git clone ssh://`.
3. Once cloned, remove the _remote_ (so that every time you push to your repository, you don't push to this very repository):
`cd project_name; git remote rm origin`, and add _remote_ to your repository (you can find the correct remote address in gitlab) **TODO: add screenshot**.
4. Modify site's settings (`_config.yml`) to match your needs. Refer to the next section for help.
5. Modify the index page. Modify (or delete) help and about pages. Add your own content.
6. Commit and push to the repository.
7. If you want to have your page publicly available, make a ticket to SIU.
8. Your page is published! Go to `https://<namespace>` in your favourite browser, or the URL you specified in the SIU ticket.
## What should you change in settings file?
* `baseurl` - this is very important. Set it to the name of the project (i.e. repository name). Here it's `pages-jekyll-lcsb-template`
* `title` field
* `e-mail` field
* `description` field
* `date` field
* `banner` field - if you want to have your own banner (the text next to _uni.lu_ logo), send us an email.
## Testing the web page locally
You can test your website locally (on your machine).
* First, make sure that you have Ruby installed. If not - please [install it](
* Then, install _bundler_ - `gem install bundler`.
* Next, initialize the site: `bundle install`.
* Finally, run the site: `bundle exec jekyll serve`.
## Common problems
### *The website looks broken! There are no images, no colors etc.*
You probably didn't configure `baseurl` parameter in the settings. Please take a look on `_settings.yml` file.
### *The links in the menu are not working (they point to "404: Not found").*
You probably didn't add `permalink` attribute. Or the post has `published: false` or `draft: true` set. Please take a look on the post file.
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# Reproducibility
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