.ci/add-timestamp-to-howtocard.sh

+#!/bin/sh
+
+# change this with environment
+DEFAULT_NOT_SOURCE_REGEX="/\\/assets\\//"
+NOT_SOURCE_REGEX="${NOT_SOURCE_REGEX:-$DEFAULT_NOT_SOURCE_REGEX}"
+TIMESTAMP_SUFFIX="${SUFFIX:-.timestamp}"
+LOGFILE="${LOGFILE:-/dev/null}"
+
+[ -z "$1" ] && echo "$0: no inputs specified?" >/dev/stderr
+
+while [ -n "$1" ]
+do
+	echo "sourcing directory '$1' ..." >> "$LOGFILE"
+	find "$1" -type f -name '*.md' | grep -v "$NOT_SOURCE_REGEX" | while read file ; do
+		fn=`basename "$file"`
+		dir=`dirname "$file"`
+		tsfn="$fn.timestamp"
+		(
+			echo "making timestamp in '$dir' for file '$fn' ..." >> "$LOGFILE"
+			cd "$dir"
+			if [ -f "$tsfn" ]
+			then echo "... but it already exists; skipping!" >> "$LOGFILE"
+			else
+				TIMESTAMP=`git log -n 1 --pretty=format:%cs -- "$fn"`
+				mv "$fn" "$fn.temporary"
+				head -n1 "$fn.temporary" > "$fn"
+				echo "timestamp: \"$TIMESTAMP\"" >> "$fn"
+				tail -n+2 "$fn.temporary" >> "$fn"
+				rm -f "$fn.temporary"
+			fi
+		)
+	done
+	shift
+done

generator @ 53a922a1

-Subproject commit e7924d5dc59143e62d60ea4e0ed844db204e71a7
+Subproject commit 53a922a13c4e8916c97599b5242493a47ea0a2e2

.gitattributes

-*.PNG filter=lfs diff=lfs merge=lfs -text
-*.png filter=lfs diff=lfs merge=lfs -text
-*.jpg filter=lfs diff=lfs merge=lfs -text
-*.jpeg filter=lfs diff=lfs merge=lfs -text
-*.mp4 filter=lfs diff=lfs merge=lfs -text

.gitlab-ci.yml

@@ -11,6 +11,7 @@ stages:
 
 variables:
     GIT_STRATEGY: clone
+    GIT_DEPTH: 0
     DOCKER_DRIVER: overlay2
     DOCKER_TLS_CERTDIR: ""
     GIT_SUBMODULE_STRATEGY: recursive
@@ -77,7 +78,7 @@ build:pages:
   stage: build
   variables:
     JEKYLL_ENV: production
-    BUNDLER_VERSION: 2.0.2
+    BUNDLER_VERSION: 2.1.4
   artifacts:
     expire_in: 1 day
     paths:
@@ -108,6 +109,7 @@ build:pages:
     - |
       echo "Configuration: " && cat ".ci/_config_$CI_COMMIT_REF_NAME.yml"
     # Run Jekyll with custom configuration
+    - LOGFILE=/dev/stdout .ci/add-timestamp-to-howtocard.sh external
     - bundle exec jekyll build -d build --config "_config.yml,.ci/_config_$CI_COMMIT_REF_NAME.yml"
 
 # check
@@ -174,7 +176,7 @@ deploy:vm:
     - echo "$KNOWNHOSTS" > ~/.ssh/known_hosts
     - chmod 644 ~/.ssh/known_hosts
   rules:
-    - if: '$CI_PIPELINE_SOURCE != "merge_request_event" && $CI_COMMIT_REF_NAME == "develop" && $CI_PROJECT_PATH == "R3/howto-cards"'
+    #- if: '$CI_PIPELINE_SOURCE != "merge_request_event" && $CI_COMMIT_REF_NAME == "develop" && $CI_PROJECT_PATH == "R3/howto-cards"'
     - if: '$CI_PIPELINE_SOURCE != "merge_request_event" && $CI_COMMIT_REF_NAME == "master" && $CI_PROJECT_PATH == "R3/howto-cards"'
   script:
     - ssh -p $SSHPORT $SSHCONNECT "mkdir -p ~/$CI_COMMIT_REF_NAME/sources/public/$CI_JOB_ID ~/$CI_COMMIT_REF_NAME/public"

Gemfile

@@ -12,7 +12,7 @@ gem "jekyll", "~> 4.0"
 gem "bundler", "> 2.0"
 
 gem "minima", "~> 2.5"
-gem 'jekyll-theme-lcsb-default', '~> 0.4.21'
+gem 'jekyll-theme-lcsb-default', '~> 0.5.0'
 
 # If you want to use GitHub Pages, remove the "gem "jekyll"" above and
 # uncomment the line below. To upgrade, run `bundle update github-pages`.

_includes/footer.html

@@ -10,6 +10,10 @@
 
           {% comment %}This is used to generate share URL for howto-pages{% endcomment %}
           <div class="footer-text-container">
+          {% if page.timestamp %}
+            <p>Last page modification: {{ page.timestamp }}</p>
+          {% endif %}
+
           {% if page.shortcut %}
               <p>
                   Share this page:
@@ -44,4 +48,4 @@
   </footer>
   {% if site.siteID > 0 %}
       {%- include gdpr-banner.html -%}
-  {% endif %}
+  {% endif %}
\ No newline at end of file

assets/js/box_hider.js

@@ -24,7 +24,7 @@ window.boxHider = (function() {
     function GetSelectedBoxElement(id) {
         var allBoxesArray = GetAllBoxElementsArray();
         // note: handbook and lab are actually grouped sections
-        if (id.startsWith('handbook') || id.startsWith('lab') || id.startsWith('qms')) {
+        if (id.startsWith('handbook') || id.startsWith('lab') || id.startsWith('qms') || id.startsWith('publication')) {
             return true;
         } else {
             var element = document.getElementById(id);
@@ -104,6 +104,14 @@ window.boxHider = (function() {
                     ShowElement(box);
                 }
             });
+        } else if (boxId.startsWith('publication')) {
+            allBoxes.map(function(box) {
+                if (!box.id.startsWith('publication')) {
+                    HideElement(box);
+                } else {
+                    ShowElement(box);
+                }
+            });
         } else {
             allBoxes.map(function(box) {
                 if (box != selectedBox) {

cards.md

@@ -37,7 +37,8 @@ order: -1
 			<li><a href="{{ 'external/access/harrenhal-access' | relative_url }}">HARRENHAL access</a></li>
 			<li><a href="{{ 'external/access/lums-passwords' | relative_url }}">LUMS account</a></li>
 			<li><a href="{{ 'external/access/passwords' | relative_url }}">Managing your passwords</a></li>
-			<li><a href="{{ 'external/access/vpn-cerbere-access' | relative_url }}">VPN/CERBERE connection</a></li>
+			<li><a href="{{ 'external/access/vpn-access' | relative_url }}">VPN connection</a></li>
+			<li><a href="{{ 'external/access/vpn-cerbere-access' | relative_url }}">Connect to Cerbere via VPN</a></li>
 			<li><a href="{{ 'external/access/vpn-mobile' | relative_url }}">VPN connection on your mobile phone</a></li>
 			<li><a href="{{ 'external/access/wifiNetworkAccessGuests' | relative_url }}">WiFi network access for guests</a></li>
 		</ul>
@@ -56,6 +57,8 @@ order: -1
 			<li><a href="{{ 'external/contribute/markdown' | relative_url }}">Markdown</a></li>
 			<li><a href="{{ 'external/contribute/mirror-fork' | relative_url }}">Mirror fork automatically</a></li>
 			<li><a href="{{ 'external/contribute/review' | relative_url }}">Reviewing in Git</a></li>
+			<li><a href="{{ 'external/contribute/ssh-key-generation' | relative_url }}">Key-based Authentication on GitLab</a></li>
+			<li><a href="{{ 'external/contribute/supersede' | relative_url }}">Take over a stale merge request</a></li>
 			<li><a href="{{ 'external/contribute/vscode' | relative_url }}">Contribute using Visual Studio Code</a></li>
 			<li><a href="{{ 'external/contribute/web-ide' | relative_url }}">Contribute using Gitlab Web IDE</a></li>
 
@@ -64,10 +67,13 @@ order: -1
 	<div class="index-box noborderbox" id="exchange-channels-card">
 		<h3>Exchange channels</h3>
 		<ul>
-			<li><a href="{{ 'external/exchange-channels/lft' | relative_url }}">LCSB file transfer (LFT) Quick Guide</a></li>
-			<li><a href="{{ 'external/exchange-channels/calendar' | relative_url }}">Sharing calendar in Microsoft Exchange</a></li>
 			<li><a href="{{ 'external/exchange-channels/asperaweb' | relative_url }}">AsperaWEB Quick Guide</a></li>
+			<li><a href="{{ 'external/exchange-channels/atlas-hpc' | relative_url }}">Data transfer between Atlas and UL HPC Clusters</a></li>
+			<li><a href="{{ 'external/exchange-channels/calendar' | relative_url }}">Sharing calendar in Microsoft Exchange</a></li>
+			<li><a href="{{ 'external/exchange-channels/cryptomator' | relative_url }}">Cryptomator</a></li>
+			<li><a href="{{ 'external/exchange-channels/lft' | relative_url }}">LCSB file transfer (LFT) Quick Guide</a></li>
 			<li><a href="{{ 'external/exchange-channels/owncloud' | relative_url }}">Owncloud</a></li>
+
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="general-card">
@@ -86,49 +92,67 @@ order: -1
 		<h3>Integrity</h3>
 		<ul>
 			<li><a href="{{ 'external/integrity/checksum' | relative_url }}">Ensuring Integrity of Data Files with Checksums</a></li>
-			<li><a href="{{ 'external/integrity/encryption/cloud' | relative_url }}">Data upload to cloud</a></li>
+			<li><a href="{{ 'external/integrity/dmp' | relative_url }}">Data Management Plan</a></li>
 			<li><a href="{{ 'external/integrity/encryption/disk' | relative_url }}">Encrypting the Startup Disk for Your Laptop/Desktop</a></li>
 			<li><a href="{{ 'external/integrity/encryption/file' | relative_url }}">Encrypting Files and Folders</a></li>
 			<li><a href="{{ 'external/integrity/naming' | relative_url }}">Naming files</a></li>
 			<li><a href="{{ 'external/integrity/organization' | relative_url }}">Organization</a></li>
 			<li><a href="{{ 'external/integrity/sanitisation' | relative_url }}">Sanitising Data Files</a></li>
 			<li><a href="{{ 'external/integrity/spreadsheets' | relative_url }}">Working with spreadsheets</a></li>
+			<li><a href="{{ 'external/integrity/transfer/owncloud-privatebin' | relative_url }}">Transfer of Human Data with OwnCloud</a></li>
 
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="lab-equipment-card">
 		<h3>Lab: Equipment</h3>
 		<ul>
-			<li><a href="{{ 'external/lab-equipment/cryostorage' | relative_url }}">Utilization of the cryostorage</a></li>
-			<li><a href="{{ 'external/lab-equipment/dishwasher-utilization-and-maintenance' | relative_url }}">Dishwasher utilization and maintenance</a></li>
-			<li><a href="{{ 'external/lab-equipment/hoods' | relative_url }}">Laminar Flow - Fume Hood - Biosafety Cabinet: what are the differences and when to use them?</a></li>
-			<li><a href="{{ 'external/lab-equipment/lightcycler' | relative_url }}">How to leave virtual instrument mode on the LightCycler</a></li>
-			<li><a href="{{ 'external/lab-equipment/maintenance-of-fridges' | relative_url }}">Maintenance of fridges and freezers</a></li>
-			<li><a href="{{ 'external/lab-equipment/maintenance_of_cold_traps' | relative_url }}">Maintenance of cold traps  </a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-autoclaves' | relative_url }}">Utilization of autoclaves</a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-balances' | relative_url }}">Utilization of balances</a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-bsc' | relative_url }}">Biosafety Cabinets: good practices</a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-pH-meter' | relative_url }}">Utilization of pH meter</a></li>
+			<li><a href="{{ 'external/lab-equipment/autoclaves' | relative_url }}">Autoclaves: utilization</a></li>
+			<li><a href="{{ 'external/lab-equipment/balances' | relative_url }}">Balances: utilization and maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/biosafety-cabinets' | relative_url }}">Biosafety Cabinets: good practices</a></li>
+			<li><a href="{{ 'external/lab-equipment/cold-traps' | relative_url }}">Cold traps: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/cryostorage' | relative_url }}">Cryostorage: utilization</a></li>
+			<li><a href="{{ 'external/lab-equipment/dishwasher-utilization-and-maintenance' | relative_url }}">Dishwasher: utilization and maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/electric-car' | relative_url }}">Electric Car</a></li>
+			<li><a href="{{ 'external/lab-equipment/freezers' | relative_url }}">-20°C Freezers: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/freezers-80' | relative_url }}">-80°C freezers: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/freezers-150' | relative_url }}">-150°C freezers: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/fridges' | relative_url }}">Fridges: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/hoods' | relative_url }}">Hoods: Laminar Flow - Fume Hood - Biosafety Cabinet</a></li>
+			<li><a href="{{ 'external/lab-equipment/incubators' | relative_url }}">Incubators: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/lightcycler' | relative_url }}">LightCycler: leave the virtual instrument mode</a></li>
+			<li><a href="{{ 'external/lab-equipment/pH-meter' | relative_url }}">pH meter: utilization and maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/power-consumption' | relative_url }}">Power consumption of the equipment</a></li>
+
+		</ul>
+	</div>
+	<div class="index-box noborderbox" id="lab-good-practice-card">
+		<h3>Lab: Good Practice</h3>
+		<ul>
+			<li><a href="{{ 'external/lab-good-practice/mycoplasma' | relative_url }}">Mycoplasma contamination check</a></li>
 
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="lab-hsa-card">
 		<h3>Lab: Health & Safety, Access</h3>
 		<ul>
+			<li><a href="{{ 'external/lab-hsa/diphoterine' | relative_url }}">Diphoterine: utilization</a></li>
 			<li><a href="{{ 'external/lab-hsa/handwashing' | relative_url }}">Handwashing</a></li>
 			<li><a href="{{ 'external/lab-hsa/lab-coats' | relative_url }}">Lab coats</a></li>
 			<li><a href="{{ 'external/lab-hsa/personal-alert-safety-system' | relative_url }}">Personal alert safety system (PASS)</a></li>
-			<li><a href="{{ 'external/lab-hsa/shipment' | relative_url }}">Shipment of a biological or chemical sample</a></li>
-			<li><a href="{{ 'external/lab-hsa/spill-bsc' | relative_url }}">How to deal with a spill in a BSC</a></li>
-			<li><a href="{{ 'external/lab-hsa/waste' | relative_url }}">Chemical and Biological Waste Management</a></li>
+			<li><a href="{{ 'external/lab-hsa/pictograms' | relative_url }}">Pictograms</a></li>
+			<li><a href="{{ 'external/lab-hsa/ppe' | relative_url }}">Personal Protective Equipment (PPE)</a></li>
+			<li><a href="{{ 'external/lab-hsa/shipment' | relative_url }}">Shipment of biological or chemical samples with carrier</a></li>
+			<li><a href="{{ 'external/lab-hsa/spill' | relative_url }}">Spill in a laboratory</a></li>
+			<li><a href="{{ 'external/lab-hsa/spill-bsc' | relative_url }}">Spill in a Biosafety Cabinet</a></li>
+			<li><a href="{{ 'external/lab-hsa/waste' | relative_url }}">Waste Management: Chemical and Biological waste</a></li>
 
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="lab-quarks-card">
 		<h3>Lab: Quarks</h3>
 		<ul>
-			<li><a href="{{ 'external/lab-quarks/book-lab-equipment' | relative_url }}">How to book a Lab Equipment in Quarks</a></li>
-			<li><a href="{{ 'external/lab-quarks/quarks-general' | relative_url }}">Quarks - General information</a></li>
+			<li><a href="{{ 'external/lab-quarks/book-lab-equipment' | relative_url }}">Booking of a Lab Equipment</a></li>
+			<li><a href="{{ 'external/lab-quarks/general' | relative_url }}">General information on Quarks</a></li>
 
 		</ul>
 	</div>
@@ -143,12 +167,17 @@ order: -1
 	<div class="index-box noborderbox" id="publication-card">
 		<h3>Publication</h3>
 		<ul>
-			<li><a href="{{ 'external/publication/publish-repo' | relative_url }}">Publish a repository</a></li>
-			<li><a href="{{ 'external/publication/add-gitignore' | relative_url }}">Add a .gitignore to your repository</a></li>
 			<li><a href="{{ 'external/publication/orcid' | relative_url }}">Obtain an ORCID</a></li>
-			<li><a href="{{ 'external/publication/publishInBiotools' | relative_url }}">Publishing a tool in *bio.tools*</a></li>
 			<li><a href="{{ 'external/publication/phdThesisTemplate' | relative_url }}">LaTeX template for a doctoral thesis at University of Luxembourg</a></li>
 			<li><a href="{{ 'external/publication/10WaysImproveEnglish' | relative_url }}">10 ways to improve your English</a></li>
 		</ul>
 	</div>
+	<div class="index-box noborderbox" id="publication-code-card">
+		<h3>Publication: Publishing code and programs</h3>
+		<ul>
+			<li><a href="{{ 'external/publication-code/publish-repo' | relative_url }}">Publish a repository</a></li>
+			<li><a href="{{ 'external/publication-code/add-gitignore' | relative_url }}">Add a .gitignore to your repository</a></li>
+			<li><a href="{{ 'external/publication-code/publishInBiotools' | relative_url }}">Publishing a tool in *bio.tools*</a></li>
+		</ul>
+	</div>
 </div><br><center><a href="{{ '/' | relative_url }}">go back</a></center><br><center><a href="{{ '/cards' | relative_url }}">Overview of all HowTo cards</a></center>
\ No newline at end of file

external/access/lums-passwords/lums-passwords.md

@@ -32,7 +32,7 @@ This serves for internal authentication for resources provided by the LCSB, e.g.
 
 ## Requesting LUMS account as external collaborator, UL members or  UL student
 
-* In case you are not a member of LCSB/DLSM, please ask your collaborator at LSCB/DLSM to request the account for you. You will need to provide an institutional email address. 
+* In case you are not a member of LCSB/DLSM, please ask your collaborator at LCSB/DLSM to request the account for you. You will need to provide an institutional email address. 
 * Once the account is created, you will receive an email with your new LUMS account details and how to access services and VMS.
 
 ## Requesting LUMS account for externals collaborators, UL members or UL students