Initial commit

Frozen/imp.md

+---
+layout: default
+order: -1
+title: Imp
+permalink: /Frozen/imp
+---
+
+Test IMP

Frozen/smartr.md

+---
+layout: default
+order: -1
+title: Smartr
+permalink: /Frozen/smartr
+---
+
+Test Frozen

Gemfile.lock

@@ -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)
 
 PLATFORMS
+  ruby
   x64-mingw32
 
 DEPENDENCIES
-  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)
   tzinfo-data
-  wdm (~> 0.1.0)
 
 BUNDLED WITH
    1.16.4

Websites.md

+---
+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](https://minerva.pages.uni.lu/doc/)
+
+ SYSCID Data Management Plan Information Collection
+
+ CaSiAn CaSiAn Website

_config.yml

@@ -13,13 +13,13 @@
 # you will see them accessed via {{ site.title }}, {{ site.email }}, 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.
-email: your-email@example.com
+title: R3.
+email: lcsb-sysadmins@example.com
 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. http://example.com
 
 banner: default  # When you have custom images, change this setting's value to the name of the folder containing them

about.md

----
-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 [jekyllrb.com](https://jekyllrb.com/)
-
-You can find the source code for this them at Gitlab:
-[core-services/jekyll-theme-lcsb-default](https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default).
-
-We have successfully helped in publishing the following websites:
- * [Page of theme](https://core-services.pages.uni.lu/jekyll-theme-lcsb-default/)
- * [This very page](https://core-services.pages.uni.lu/pages-jekyll-lcsb-template/)
- * [Minerva doc's](https://minerva.pages.uni.lu/doc/)
- * [PDmap blog](https://pdmap.pages.uni.lu/blog/)
- * [IMP](https://imp.pages.uni.lu/web/)
\ No newline at end of file

frozen.md

+---
+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](https://git-r3lab.uni.lu).

help.md

----
-layout: page
-title: Help
-permalink: /the-help/
-order: 3
----
-
-If you need help, don't hesitate to send us an email.
\ No newline at end of file

index.md

@@ -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](https://git-r3lab.uni.lu/core-services/pages-jekyll-lcsb-template).
-Additionally, you can also navigate to the [repository for theme](https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default).
-
-# Setting up your web page
-
-## The process
-0. Make sure that you have access to [gitlab](https://git-r3lab.uni.lu/). 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](https://git-r3lab.uni.lu/projects/new). 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>.pages.uni.lu/<project_name>` convention.
-2. Clone this very repository: `git clone ssh://git@git-r3lab-server.uni.lu:8022/core-services/pages-jekyll-lcsb-template.git`.
-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>.pages.uni.lu/name-of-repository` in your favourite browser, or the URL you specified in the SIU ticket.
-
-## What should you change in settings file?
-Mandatory:
- * `baseurl` - this is very important. Set it to the name of the project (i.e. repository name). Here it's `pages-jekyll-lcsb-template`
- 
-Optional:
- * `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](https://www.ruby-lang.org/en/downloads/).
-* 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.
\ No newline at end of file
+# Reproducibility