Commit f0781141 authored by Laurent Heirendt's avatar Laurent Heirendt
Browse files

Merge branch 'update-url' into 'master'

Update url for gitlab

See merge request !80
parents 3427348b 09d65590
Pipeline #44569 passed with stages
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# In case something goes horribly wrong, you can fall back to `image: ruby:latest`
image: git-r3lab.uni.lu:4567/r3/docker/jekyll-lcsb:1.6
image: $CI_REGISTRY/r3/docker/jekyll-lcsb:1.6
stages:
- build
......
......@@ -2,16 +2,16 @@
This is a repository containing source for the index pages of [http://r3lab.uni.lu/](http://r3lab.uni.lu/) and its frozen pages.
Note that the sites from _Websites_ menu tab, are contained in their own repositories:
* TGM-pipeline at [https://git-r3lab.uni.lu/core-services/r3lab/tgm-pipeline-doc]()
* CASian at [https://git-r3lab.uni.lu/core-services/r3lab/casian-doc](https://git-r3lab.uni.lu/core-services/r3lab/casian-doc)
* IMP at [https://git-r3lab.uni.lu/core-services/r3lab/imp-doc](https://git-r3lab.uni.lu/core-services/r3lab/imp-doc)
* TGM-pipeline at [https://gitlab.lcsb.uni.lu/core-services/r3lab/tgm-pipeline-doc]()
* CASian at [https://gitlab.lcsb.uni.lu/core-services/r3lab/casian-doc](https://gitlab.lcsb.uni.lu/core-services/r3lab/casian-doc)
* IMP at [https://gitlab.lcsb.uni.lu/core-services/r3lab/imp-doc](https://gitlab.lcsb.uni.lu/core-services/r3lab/imp-doc)
# Deployment
## How are the pages built?
All of these pages are built with Jekyll using Gitlab-CI (see respective `.gitlab-ci.yml` files and the instructions on [https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default](https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-default)` if you need more information).
All of these pages are built with Jekyll using Gitlab-CI (see respective `.gitlab-ci.yml` files and the instructions on [https://gitlab.lcsb.uni.lu/core-services/jekyll-theme-lcsb-default](https://gitlab.lcsb.uni.lu/core-services/jekyll-theme-lcsb-default)` if you need more information).
## How are the pages uploaded to the VM?
There is `deploy to production` section in `.gitlab-ci.yml`, which pushes the built webpage onto the VM. Under the hood, there are details saved in [Settings ==> CI/CD ==> Variables](https://git-r3lab.uni.lu/core-services/r3lab/r3-pages/-/settings/ci_cd) section, which comprise the secret values (SSH key, the username, VM address etc.). If you create a new page which should upload the page there, don't forget to add those!
There is `deploy to production` section in `.gitlab-ci.yml`, which pushes the built webpage onto the VM. Under the hood, there are details saved in [Settings ==> CI/CD ==> Variables](https://gitlab.lcsb.uni.lu/core-services/r3lab/r3-pages/-/settings/ci_cd) section, which comprise the secret values (SSH key, the username, VM address etc.). If you create a new page which should upload the page there, don't forget to add those!
## How are the pages published?
At current moment, the staticpages VM is configured to expose files from `/home/r3pages/web/latest` under `r3lab.uni.lu`.
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......@@ -8,7 +8,7 @@ permalink: /frozen/
# Information
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/core-services/r3-pages).
This website is under version control on the [LCSB Gitlab](https://gitlab.lcsb.uni.lu/core-services/r3-pages).
# Frozen pages
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......@@ -21,7 +21,7 @@ The data is available <a href="https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?t
{% rblock source code %}
The source code is available <a href="https://git-r3lab.uni.lu/eci/shinyscreen/-/tree/v.0.1.1-paper">here</a>.
The source code is available <a href="https://gitlab.lcsb.uni.lu/eci/shinyscreen/-/tree/v.0.1.1-paper">here</a>.
{% endrblock %}
{% endrgridblock %}
......
......@@ -9,7 +9,7 @@ permalink: /frozen/imp
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*
{% endrtitle %}
{% endrtitle %}
{% rgridblock a-unique-id %}
{% rblock Website | fas fa-globe %}
......@@ -17,11 +17,11 @@ The **IMP** website hosted within *R3lab* frame is available [here](https://r3la
{% 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.
The source code of IMP is available on the [LCSB Gitlab](https://gitlab.lcsb.uni.lu/IMP/IMP) where you can traceback what have been done by the authors.
{% endrblock %}
{% 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).
Some additionnal analysis made on the paper as also available on the [LCSB Gitlab](https://gitlab.lcsb.uni.lu/IMP/IMP_manuscript_analysis).
{% endrblock %}
{% rblock Workflow | fas fa-cogs %}
......
......@@ -26,9 +26,9 @@ The dataset is available <a href="https://webdav-r3lab.uni.lu/public/data/mitomo
{% rblock Source code | fas fa-code %}
The source code is available on the <a href="https://git-r3lab.uni.lu/guadalupe.garcia/mitochondria-morphology">LCSB Gitlab</a> where you can traceback what have been done by the authors.
The source code is available on the <a href="https://gitlab.lcsb.uni.lu/guadalupe.garcia/mitochondria-morphology">LCSB Gitlab</a> where you can traceback what have been done by the authors.
{% endrblock %}
{% endrgridblock %}
{% endrgridblock %}
......@@ -26,9 +26,9 @@ The dataset is available <a href="https://webdav-r3lab.uni.lu/public/data/mitomo
{% rblock Source code | fas fa-code %}
The source code is available on the <a href="https://git-r3lab.uni.lu">LCSB Gitlab</a> where you can traceback what have been done by the authors.
The source code is available on the <a href="https://gitlab.lcsb.uni.lu">LCSB Gitlab</a> where you can traceback what have been done by the authors.
{% endrblock %}
{% endrgridblock %}
{% endrgridblock %}
......@@ -7,17 +7,17 @@ permalink: /frozen/q3g1-7a85
{% rtitle Agent-based SEIR-ICU model for Luxembourg %}
Atte Aalto, Laurent Mombaerts, Laurent Heirendt, Christophe Trefois, Daniele Proverbio, Françoise Kemp, Jorge Gonçalves, Alexander Skupin
{% endrtitle %}
{% endrtitle %}
{% rgridblock a-unique-id %}
{% rblock Source code %}
Source code is hosted on Gitlab [Gitlab](https://git-r3lab.uni.lu/SCG/seir-icu).
Source code is hosted on Gitlab [Gitlab](https://gitlab.lcsb.uni.lu/SCG/seir-icu).
{% endrblock %}
{% rblock Artificial data %}
The used real data cannot be shared due to data protection reasons. An artificial, generated social network data can be found here (households and regional information is not included).
{% endrblock %}
{% endrgridblock %}
{% endrgridblock %}
......@@ -19,7 +19,7 @@ The complete dataset is available [here](https://webdav-r3lab.uni.lu/public/data
{% endrblock %}
{% rblock source code %}
The source code used to make the analysis/figures of the publication is available on [Gitlab](https://git-r3lab.uni.lu/LCSB-CEN/cloneclassifier).
The source code used to make the analysis/figures of the publication is available on [Gitlab](https://gitlab.lcsb.uni.lu/LCSB-CEN/cloneclassifier).
{% endrblock %}
{% endrgridblock %}
\ No newline at end of file
......@@ -23,7 +23,7 @@ The previously published data is available at ERR2984773 and ERR2887847, SRR7585
{% rblock source code %}
The source code is available <a href="https://git-r3lab.uni.lu/ESB/ont_pilot_gitlab">here</a>.
The source code is available <a href="https://gitlab.lcsb.uni.lu/ESB/ont_pilot_gitlab">here</a>.
{% endrblock %}
{% endrgridblock %}
......
......@@ -22,7 +22,7 @@ The documentation of **COBREXA.jl** is available [here](https://lcsb-biocore.git
{% endrblock %}
{% rblock benchmarks | fas fa-code %}
The benchmark scripts are available [here](https://git-r3lab.uni.lu/R3/outreach/papers/cobrexa/benchmarks).
The benchmark scripts are available [here](https://gitlab.lcsb.uni.lu/R3/outreach/papers/cobrexa/benchmarks).
{% endrblock %}
{% endrgridblock %}
......@@ -31,34 +31,34 @@ Here you can find a collection of tools used @LCSB to provide support for reprod
<div style="display: flex; flex-wrap: wrap">
<div class="block">
<div class="image-box">
<a href="https://git-r3lab.uni.lu/">
<img src="{{ "images/gitlab-logo.png" | relative_url }}" width="120px" />
<a href="https://gitlab.lcsb.uni.lu/">
<img src="{{ "images/gitlab-logo.png" | relative_url }}" width="120px" />
</a>
</div>
<a href="https://git-r3lab.uni.lu/"><strong>Gitlab</strong></a> is an open source software that provide Version control and many other usefule features for devellopers and scientists.
</div>
<a href="https://gitlab.lcsb.uni.lu/"><strong>Gitlab</strong></a> is an open source software that provide Version control and many other usefule features for devellopers and scientists.
</div>
<div class="block">
<div class="image-box">
<div class="image-box">
<a href="https://owncloud.lcsb.uni.lu/">
<img src="{{ "images/owncloud-logo.png" | relative_url }}" width="150px" />
<img src="{{ "images/owncloud-logo.png" | relative_url }}" width="150px" />
</a>
</div>
<a href="https://owncloud.lcsb.uni.lu/"><strong>OwnCloud</strong></a> is an online file sharing platform that makes collaboration over documents easier.
</div>
<div class="block">
<div class="image-box">
<div class="image-box">
<a href="https://asperaweb.lcsb.uni.lu/">
<img src="{{ "images/aspera-logo.png" | relative_url }}" width="180px" />
<img src="{{ "images/aspera-logo.png" | relative_url }}" width="180px" />
</a>
</div>
<a href="https://asperaweb.lcsb.uni.lu/"><strong>AsperaWEB</strong></a> is hi-speed file transfer software, allowing for efficient exchange of very large files.
</div>
<div class="block">
<div class="image-box">
<div class="block">
<div class="image-box">
<a href="https://webdav-r3lab.uni.lu/">
<img src="{{ "images/webdav-logo.png" | relative_url }}" width="150px" />
<img src="{{ "images/webdav-logo.png" | relative_url }}" width="150px" />
</a>
</div>
<a href="https://webdav-r3lab.uni.lu/"><strong>WEBDAV</strong></a> is a file sharing system over the web that brings more advanced security and control that a traditionnal FTP server.
<a href="https://webdav-r3lab.uni.lu/"><strong>WEBDAV</strong></a> is a file sharing system over the web that brings more advanced security and control that a traditionnal FTP server.
</div>
</div>
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