Merge branch 'develop' into 'master'

Regular merge of develop

See merge request !41

.ci/.autoRedirect

@@ -14,7 +14,12 @@
             }
         });
     }
-    UrlExists('https://r3-core.pages.uni.lu/howto-cards-internal/index.html', function(status){
+
+    // define URLs
+    var internalURL = 'https://r3-core.pages.uni.lu/howto-cards-internal';
+    var externalURL = 'https://r3.pages.uni.lu/howto-cards';
+
+    UrlExists(internalURL+'/index.html', function(status){
         var s = window.location.href;
         var pathArray = s.split('?');
 
@@ -28,22 +33,38 @@
         if(status === 200){
             // internal pages
             if (sub.length > 0) {
-                UrlExists('https://r3-core.pages.uni.lu/howto-cards-internal/stable/internal/'+sub, function(status){
-                    // redirect if card is actually internal and exists
-                    if (status == 200) {
-                        window.location.href = 'https://r3-core.pages.uni.lu/howto-cards-internal/stable/internal/'+sub;
+                UrlExists(internalURL+'/stable/internal/'+sub, function(status){
+                    if (status == 200) { // if sub-card is internal in the internal directory and exists
+                        window.location.href = internalURL+'/stable/internal/'+sub;
                     } else {
-                        window.location.href = 'https://r3-core.pages.uni.lu/howto-cards-internal/stable/external/'+sub;
+                        UrlExists(internalURL+'/stable/external/'+sub, function(status){
+                            if (status == 200) { // if sub-card is internal in the external directory and exists
+                                window.location.href = internalURL+'/stable/external/'+sub;
+                            } else {
+                                window.location.href = internalURL+'/404.html';
+                            }
+                        });
                     }
                 });
             } else {
-                window.location.href = 'https://r3-core.pages.uni.lu/howto-cards-internal/stable/'+sub;
+                UrlExists(internalURL+'/stable', function(status){
+                    if (status == 200) { // if card is internal and exists
+                        window.location.href = internalURL+'/stable';
+                    } else {
+                        window.location.href = internalURL+'/404.html';
+                    }
+                });
             }
-
+        // external pages
         } else {
-            // external pages
             if (sub.length > 0) { sub = 'external/'+sub; }
-            window.location.href = 'https://r3.pages.uni.lu/howto-cards/stable/'+sub;
+            UrlExists(externalURL+'/stable/'+sub, function(status){
+                if (status == 200) { // if sub-car is internal and exists
+                    window.location.href = externalURL+'/stable/'+sub;
+                } else {
+                    window.location.href = externalURL+'/404.html';
+                }
+            });
         }
     });
     </script>

.ci/deploy.sh

@@ -17,6 +17,11 @@ for branch in $(git for-each-ref --format='%(refname:strip=3)' refs/remotes); do
 
     # build the website
     bundle exec jekyll build --baseurl="howto-cards/$artefact" -d "public/$artefact"
+
+    if [[ $branch == "master" ]]; then
+        # set the 404
+        cp howto-cards/$artefact/404.html public/404.html
+    fi
 done
 
 # checkout the current branch

external/exchange-channels/duma.md

@@ -16,7 +16,7 @@ An access link can be reached via standard web browsers. Data can be transferred
 * Through the web browser by visiting the link, which is our recommended way of data transfer, described in this [section of the guide](#ASPERAWEB_WEB)
 * Through the use of a command line tool. If your data sits in an environment, where you can not launch a web browser, then you may use use a command line client tool to reach an access link. This process is described in this [section of this guide](#ASPERAWEB_CLI).
 
-The use of DUMA is mediated by LCSB's data stewards. If you require assistance in using DUMA, you should send an email to [LCSB admin team](mailto:lcsb-sysadmins@uni.lu).
+The use of DUMA is mediated by LCSB's data stewards. If you require assistance in using DUMA, you should send an email to the [LCSB datastewards](mailto:lcsb-datastewards@uni.lu).
 
 <a name="ASPERAWEB_WEB"></a>
 ## Accessing AsperaWEB via Web Interface

external/git-clients/git-clients.md

+---
+layout: page
+permalink: /external/git-clients/
+---
+
+# Git clients
+
+## Installation of Git
+
+You can find installers for Windows, MacOS and Linux on the [Git webpage](https://git-scm.com/downloads).
+
+## GUI clients
+
+Here is a list of suggested Git GUI clients:
+
+* [Sourcetree](https://www.sourcetreeapp.com)
+* [Fork](https://git-fork.com)
+* [SmartGit](https://www.syntevo.com/smartgit/)
+
+You can find more clients on the [Git webpage](https://git-scm.com/downloads/guis).
+
+## IDEs
+
+There are also several IDEs (integrated development environments) that have git functionalities included:
+
+* [GitLab WebIDE](https://docs.gitlab.com/ee/user/project/web_ide/)
+* [Visual Studio Code](https://code.visualstudio.com/)
+* [Atom](https://atom.io/)
+* [IntelliJ](https://www.jetbrains.com/idea/)
+* [PyCharm](https://www.jetbrains.com/pycharm/)

index.md

@@ -14,3 +14,4 @@ Bioinformatics Core assists Luxembourg Centre for Systems Biomedicine ([LCSB](ht
   * [Registering human-subject data to DAISY](./external/daisy/)
   * [Markdown markup language](./external/markdown/)
   * [LUMS account](./external/lums-passwords)
+  * [Git clients](./external/git-clients/)