fix(ci): fixes deployment to staticpages VM

.gitlab-ci.yml

@@ -7,9 +7,7 @@ build the website:
   - gem install bundler -v2.0.2
   - bundle install && bundle update jekyll-theme-lcsb-default && bundle update jekyll-theme-lcsb-frozen-components
   script:
-  - 'echo "baseurl: /$CI_PROJECT_NAME" >> _config_ci.yml'
-  - 'echo "url: https://$CI_PROJECT_NAMESPACE.$CI_PAGES_DOMAIN" >> _config_ci.yml'
-  - bundle exec jekyll build -d build --config "_config.yml,_config_ci.yml"
+  - bundle exec jekyll build -d build --config "_config.yml,_config_staticpages.yml"
   - 'echo $CI_COMMIT_SHA > build/version'
   artifacts:
     expire_in: 3 days
@@ -18,14 +16,21 @@ build the website:
   variables:
     JEKYLL_ENV: production
 
-pages:
+
+## Deploys the website to a separate VM
+Deploy to production:
   stage: deploy
-  only:
-  - master
+  image: alpine:3.1
+  before_script:
+    - 'which ssh-agent || ( apk add --update openssh )'
+    - eval $(ssh-agent -s)
+    - echo "$SSHPRIVKEY" | tr -d '\r' | ssh-add - > /dev/null
+    - mkdir -p ~/.ssh && chmod 700 ~/.ssh
+    - 'echo -e "Host *\n\tStrictHostKeyChecking no\n\n" > ~/.ssh/config'
+    - echo "$KNOWNHOSTS" > ~/.ssh/known_hosts
+    - chmod 644 ~/.ssh/known_hosts
   script:
-  - mv build public
-  - echo "Your website is available at $CI_PAGES_URL"
-  artifacts:
-    expire_in: 1 week
-    paths:
-    - public
+    # don't forget to create ~/web/latest folder manually in the initial configuration on the VM!
+    - ssh -p $SSHPORT $SSHCONNECT "mkdir -p ~/web/web_$CI_JOB_ID"
+    - scp -P $SSHPORT -r build/* $SSHCONNECT:~/web/web_$CI_JOB_ID
+    - ssh -p $SSHPORT $SSHCONNECT "cd ~/web/latest && ln -fs ../web_$CI_JOB_ID/* . && cd .. && find . -type d -not -newermt '-1 minutes' -exec rm -rf {} +;"

_config_staticpages.yml

+baseurl: "/wesite"
+url: "https://r3lab.uni.lu"

index.md

@@ -8,5 +8,5 @@ order: 1
 Here you can find a collection of tools used @LCSB to provide support for reproducibility and transparency.
 
 ## Associated services
-| [![Gitlab]({{ "images/gitlab-logo.png" | relative_url }}){:width="120px"}](https://git-r3lab.uni.lu/){:target="_blank"}   | **Gitlab** is an open source software that provide Version control and many other usefule features for devellopers and scientists.  |
-| [![Webdav]({{ "images/webdav-logo.png" | relative_url }}){:width="120px"}](https://webdav-r3lab.uni.lu/){:target="_blank"} | **WEBDAV** is a file sharing system over the web that brings more advanced security and control that a traditionnal FTP server.  |
+|  [![Gitlab]({{ "images/gitlab-logo.png" | relative_url }}){:width="120px"}](https://git-r3lab.uni.lu/)   | **Gitlab** is an open source software that provide Version control and many other usefule features for devellopers and scientists.  |
+|  [![Webdav]({{ "images/webdav-logo.png" | relative_url }}){:width="120px"}](https://webdav-r3lab.uni.lu/) | **WEBDAV** is a file sharing system over the web that brings more advanced security and control that a traditionnal FTP server.  |

websites.md

@@ -7,12 +7,12 @@ permalink: /websites/
 
 # Websites hosted within the R3lab frame:
 
-* **[TGM pipeline](https://core-services.pages.uni.lu/tgm-pipeline-doc/){:target="_blank"}** - a platform for visually-aided exploration, analysis and interpretation of high-throughput translational medicine data
+* **[TGM pipeline](https://core-services.pages.uni.lu/tgm-pipeline-doc/)** - a platform for visually-aided exploration, analysis and interpretation of high-throughput translational medicine data
 
-* **[IMP](https://imp.pages.uni.lu/web/){:target="_blank"}** - Integrated Meta-omic Pipeline
+* **[IMP](https://imp.pages.uni.lu/web/)** - Integrated Meta-omic Pipeline
 
-* **[MINERVA](https://minerva.pages.uni.lu/doc/){:target="_blank"}** - a platform for Molecular Interaction NEtwoRk VisuAlization
+* **[MINERVA](https://minerva.pages.uni.lu/doc/)** - a platform for Molecular Interaction NEtwoRk VisuAlization
 
-* **[SYSCID](http://datacatalog.elixir-luxembourg.org/limesurvey/index.php?r=survey/index/sid/395386&lang=en){:target="_blank"}** - Data Management Plan Information Collection
+* **[SYSCID](http://datacatalog.elixir-luxembourg.org/limesurvey/index.php?r=survey/index/sid/395386&lang=en)** - Data Management Plan Information Collection
 
-* **[CaSiAn](https://core-services.pages.uni.lu/casian-doc/){:target="_blank"}** - CaSiAn Website
+* **[CaSiAn](https://core-services.pages.uni.lu/casian-doc/)** - CaSiAn Website