Merge branch 'dev' into feat/svm_best_pracices

deNBI · Apr 10, 2024 · 5acbd23 · 5acbd23
2 parents 1f35256 + af1dce7
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diff --git a/README.md b/README.md
@@ -12,13 +12,13 @@ You can find the documentation
 Use the Environment which will also be used in production.
 
 ~~~BASH
-docker run -it -v "$(pwd):/srv_root/docs"  -p "8000:8000" --env ENABLED_HTMLPROOFER=True --entrypoint="mkdocs" denbicloud/mkdocswebhook:2.5.0 serve -f /srv_root/docs/config.yml   --dev-addr 0.0.0.0:8000
+docker run -it -v "$(pwd):/srv_root/docs"  -p "8000:8000" --env ENABLED_HTMLPROOFER=True --entrypoint="mkdocs" podman pull quay.io/denbicloud/mkdocswebhook:3.3.0 serve -f /srv_root/docs/config.yml   --dev-addr 0.0.0.0:8000
 ~~~
 
 Or turn off the HTML Proffer for faster startup:
 
 ~~~BASH
-docker run -it -v "$(pwd):/srv_root/docs"  -p "8000:8000" --env ENABLED_HTMLPROOFER=False --entrypoint="mkdocs" denbicloud/mkdocswebhook:2.5.0 serve -f /srv_root/docs/config.yml   --dev-addr 0.0.0.0:8000
+docker run -it -v "$(pwd):/srv_root/docs"  -p "8000:8000" --env ENABLED_HTMLPROOFER=False --entrypoint="mkdocs" quay.io/denbicloud/mkdocswebhook:3.3.0 serve -f /srv_root/docs/config.yml   --dev-addr 0.0.0.0:8000
 ~~~
 
 ### Local

diff --git a/config.yml b/config.yml
@@ -29,10 +29,12 @@ repo_name: 'deNBI/cloud-user-docs'
 repo_url: 'https://github.com/deNBI/cloud-user-docs'
 edit_uri: blob/master/wiki/
 use_directory_urls: true
-site_url: !ENV [ SITE_URL, 'https://cloud.denbi.de/wiki/' ]
+site_url: !ENV [SITE_URL, 'https://cloud.denbi.de/wiki/']
+
 plugins:
   - search
   - glightbox
+  - macros
   - git-revision-date-localized:
       fallback_to_build_date: true
   - htmlproofer:
@@ -55,7 +57,7 @@ markdown_extensions:
   - pymdownx.betterem:
       smart_enable: all
   - pymdownx.emoji:
-      emoji_index: !!python/name:materialx.emoji.twemoji
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
       emoji_generator: !!python/name:materialx.emoji.to_svg
   - pymdownx.caret
   - pymdownx.critic
@@ -101,7 +103,8 @@ extra:
       name: de.NBI on YouTube
     - icon: fontawesome/brands/wikipedia-w
       link: https://en.wikipedia.org/wiki/German_Network_for_Bioinformatics_Infrastructure
-      name: de.NBI on Wikipedia
+      name: de.NBI on Wikipedia  
+  simplevm_wiki_link: !ENV [SIMPLE_VM_WIKI_LINK, 'https://simplevm.denbi.de/wiki/']
 
 nav:
   - 'Home': index.md
@@ -118,63 +121,44 @@ nav:
       - 'Personal Data': portal/personal_data.md
   - 'Simple VM':
       - simple_vm/index.md
-      - 'Group Permissions': simple_vm/permissions.md
-      - 'New instance': simple_vm/new_instance.md
-      - 'Instance overview': simple_vm/instance_overview.md
-      - 'Instance details': simple_vm/instance_detail.md
-      - 'Cluster':
-          - simple_vm/Cluster/index.md
-          - 'New cluster': simple_vm/Cluster/new_cluster.md
-          - 'Cluster overview': simple_vm/Cluster/cluster_overview.md
-          - 'Cluster detail': simple_vm/Cluster/cluster_detail.md
-      - 'SSH keys and sharing access': simple_vm/keypairs.md
-      - 'Volumes': simple_vm/volumes.md
-      - 'Images/Snapshots': simple_vm/snapshots.md
-      - 'Backup data': simple_vm/backup.md
-      - 'Customization': simple_vm/customization.md
-      - 'Concurrent Guacamole sessions': simple_vm/guacamole.md
-      - 'Concurrent RStudio sessions': simple_vm/rstudio.md
-      - 'Workshops': simple_vm/workshop.md
-      - 'Miscellaneous': simple_vm/misc.md
-      - 'Best Practices': simple_vm/best_practices.md
-  - 'OpenStack Quickstart': quickstart.md
-  - 'Security': security.md
-  - 'Concept':
-      - 'OpenStack Basics': Concept/basics.md
-      - 'OpenStack Components': Concept/openstack.md
-      - 'Flavors': Concept/flavors.md
-      - 'Images': Concept/images.md
-  - 'Tutorials':
-      - 'Access de.NBI Virtual Machines from Windows 10': Tutorials/Win10_SSH/index.md
-      - 'Access a SimpleVM with Mosh': Tutorials/Mosh/index.md
-      - 'Ansible Automation': Tutorials/Ansible/index.md
-      - 'Bibigrid': Tutorials/BiBiGrid/index.md
-      - 'Blast on BiBiGrid': Tutorials/BlastOnBiBiGrid/index.md
-      - 'Hybridcloud': Tutorials/Hybridcloud/index.md
-      - 'Install latest CUDA version': Tutorials/CUDA/index.md
-      - 'JupyterHub': Tutorials/JupyterHub/index.md
-      - 'Kubermatic': Tutorials/Kubermatic/index.md
-      - 'Loadbalancer': Tutorials/Loadbalancer/index.md
-      - 'Object Storage': Tutorials/ObjectStorage/index.md
-      - 'Public Web Server': Tutorials/PublicWebServer/index.md
-      - 'Reverse Proxy with Elixir AAI': Tutorials/Elixir_AAI/Elixir_AAI.md
-      - 'Save FloatingIPs': Tutorials/SaveFloatingIPs/index.md
-      - 'Set up RStudio': Tutorials/RStudio_Server/index.md
-      - 'Persistent SSH Sessions': Tutorials/Persistent_SSH_Sessions/index.md
-      - 'SimpleVM File Transfer': Tutorials/File_Transfer_Methods/index.md
-      - 'Theia Web IDE': Tutorials/TheiaIde/index.md
-      - 'UserData': Tutorials/UserData/index.md
-      - 'Using X2GO': Tutorials/X2GO/x2go.md
-  - 'FAQ': 'FAQ.md'
-  - 'Compute Center Specific':
-      - 'Berlin': Compute_Center/Berlin.md
-      - 'Bielefeld': Compute_Center/Bielefeld.md
-      - 'EMBL': Compute_Center/EMBL.md
-      - 'Freiburg': Compute_Center/Freiburg.md
-      - 'Giessen': Compute_Center/Giessen.md
-      - 'Heidelberg Uni': Compute_Center/Heidelberg.md
-      - 'Heidelberg DKFZ': Compute_Center/Heidelberg-DKFZ.md
-      - 'Tuebingen': Compute_Center/Tuebingen.md
+  - 'OpenStack Quickstart' : quickstart.md
+  - 'Security' : security.md
+  - 'Concept' :
+    - 'OpenStack Basics' : Concept/basics.md
+    - 'OpenStack Components' : Concept/openstack.md
+    - 'Flavors' : Concept/flavors.md
+    - 'Images' : Concept/images.md
+  - 'Tutorials' :
+    - 'Tutorials': Tutorials/index.md
+    - 'Access de.NBI Virtual Machines from Windows 10' : Tutorials/Win10_SSH/index.md
+    - 'Access project infrastructure with sshuttle' : Tutorials/Sshuttle/index.md
+    - 'Ansible Automation' : Tutorials/Ansible/index.md
+    - 'Bibigrid' : Tutorials/BiBiGrid/index.md
+    - 'Blast on BiBiGrid' : Tutorials/BlastOnBiBiGrid/index.md
+    - 'Hybridcloud' : Tutorials/Hybridcloud/index.md
+    - 'Install latest CUDA version' : Tutorials/CUDA/index.md
+    - 'JupyterHub' : Tutorials/JupyterHub/index.md
+    - 'Kubermatic' : Tutorials/Kubermatic/index.md
+    - 'Loadbalancer' : Tutorials/Loadbalancer/index.md
+    - 'Object Storage' : Tutorials/ObjectStorage/index.md
+    - 'Public Web Server' : Tutorials/PublicWebServer/index.md
+    - 'Reverse Proxy with Elixir AAI': Tutorials/Elixir_AAI/Elixir_AAI.md
+    - 'Save FloatingIPs' : Tutorials/SaveFloatingIPs/index.md
+    - 'Set up RStudio' : Tutorials/RStudio_Server/index.md
+    - 'Persistent SSH Sessions' : Tutorials/Persistent_SSH_Sessions/index.md
+    - 'Theia Web IDE': Tutorials/TheiaIde/index.md
+    - 'UserData' : Tutorials/UserData/index.md
+    - 'Using X2GO': Tutorials/X2GO/x2go.md
+  - 'FAQ' : 'FAQ.md'
+  - 'Compute Center Specific' :
+    - 'Berlin' : Compute_Center/Berlin.md
+    - 'Bielefeld' : Compute_Center/Bielefeld.md
+    - 'EMBL' : Compute_Center/EMBL.md
+    - 'Freiburg' : Compute_Center/Freiburg.md
+    - 'Giessen' : Compute_Center/Giessen.md
+    - 'Heidelberg Uni' : Compute_Center/Heidelberg.md
+    - 'Heidelberg DKFZ' : Compute_Center/Heidelberg-DKFZ.md
+    - 'Tuebingen' : Compute_Center/Tuebingen.md
   - 'Cloud Admin':
       - 'Configure OpenStack to use Elixir AAI via OpenID Connect': cloud_admin/elixir_OIDC.md
       - 'Register your identity provider for ELIXIR': cloud_admin/identity_provider.md

diff --git a/config_local.yml b/config_local.yml
@@ -8,6 +8,7 @@ theme:
   logo: 'img/denbi.svg'
   favicon: 'img/denbi.svg'
 repo_name: 'deNBI/cloud-user-docs'
+
 repo_url: 'https://github.com/deNBI/cloud-user-docs'
 edit_uri: blob/master/wiki/
 markdown_extensions:
@@ -43,23 +44,7 @@ nav:
     - 'Cloud Credits': portal/credits.md
     - 'Personal Data': portal/personal_data.md
   - 'Simple VM':
-      - 'Group Permissions': simple_vm/permissions.md
-      - 'New instance': simple_vm/new_instance.md
-      - 'Instance overview': simple_vm/instance_overview.md
-      - 'Instance details': simple_vm/instance_detail.md
-      - 'Cluster' :
-        - 'Cluster': simple_vm/Cluster/index.md
-        - 'New cluster': simple_vm/Cluster/new_cluster.md
-        - 'Cluster overview': simple_vm/Cluster/cluster_overview.md
-      - 'SSH keys and sharing access': simple_vm/keypairs.md
-      - 'Volumes': simple_vm/volumes.md
-      - 'Images/Snapshots': simple_vm/snapshots.md
-      - 'Backuping data': simple_vm/backup.md
-      - 'Customization': simple_vm/customization.md
-      - 'Concurrent Guacamole sessions': simple_vm/guacamole.md
-      - 'Concurrent RStudio sessions': simple_vm/rstudio.md
-      - 'Workshops': simple_vm/workshop.md
-      - 'Miscellaneous': simple_vm/misc.md
+    - simple_vm/index.md
   - 'OpenStack Quickstart' : quickstart.md
   - 'Security' : security.md
   - 'Concept' :
@@ -68,8 +53,8 @@ nav:
     - 'Flavors' : Concept/flavors.md
     - 'Images' : Concept/images.md
   - 'Tutorials' :
+    - 'Tutorials': Tutorials/index.md
     - 'Access de.NBI Virtual Machines from Windows 10' : Tutorials/Win10_SSH/index.md
-    - 'Access a SimpleVM with Mosh' : Tutorials/Mosh/index.md
     - 'Ansible Automation' : Tutorials/Ansible/index.md
     - 'Bibigrid' : Tutorials/BiBiGrid/index.md
     - 'Blast on BiBiGrid' : Tutorials/BlastOnBiBiGrid/index.md
@@ -82,7 +67,6 @@ nav:
     - 'Save FloatingIPs' : Tutorials/SaveFloatingIPs/index.md
     - 'Set up RStudio' : Tutorials/RStudio_Server/index.md
     - 'Persistent SSH Sessions' : Tutorials/Persistent_SSH_Sessions/index.md
-    - 'SimpleVM File Transfer' : Tutorials/File_Transfer_Methods/index.md
     - 'Theia Web IDE': Tutorials/TheiaIde/index.md
     - 'UserData' : Tutorials/UserData/index.md
     - 'Using X2GO': Tutorials/X2GO/x2go.md

diff --git a/wiki/Compute_Center/Berlin.md b/wiki/Compute_Center/Berlin.md
@@ -87,16 +87,17 @@ standard users for some common distributions:
 To connect via Windows 10 you can use PowerShell as OpenSSH ist already installed by default. Create the ssh config file ```$HOME\.ssh\config``` with notepad or use the PowerShell command ```Set-Content -Path $HOME\.ssh\config -Value '<add file content here>'```
 When you use PowerShell, make sure to edit the input of the file. Fill in your information and make sure that the sections HostName, IdentityFile, User, and ProxyJump are indented with four spaces for both entries.
 ```bash
+# Replace all fields in {curly braces}
 Host denbi-jumphost-01.bihealth.org
     HostName denbi-jumphost-01.bihealth.org
-    User LifeScienceLogin
-    IdentityFile PATH_TO_KEY
+    User {LifeScienceLogin}
+    IdentityFile {PATH_TO_KEY}
 
 
-Host NAME_OF_VM  # first vm
-    HostName 172.16.XXX.XXX
-    IdentityFile PATH_TO_KEY
-    User ubuntu / centos
+Host {NAME_OF_VM}  # first vm
+    HostName {172.16.XXX.XXX}
+    IdentityFile {PATH_TO_KEY}
+    User {ubuntu / centos}
     ProxyJump denbi-jumphost-01.bihealth.org
 ```
 
@@ -108,18 +109,18 @@ ssh NAME_OF_VM
 #### Linux .ssh/config
 
 ```bash
+# Replace all fields in {curly braces}
 Host denbi-jumphost-01.bihealth.org
     HostName denbi-jumphost-01.bihealth.org
-    User LifeScienceLogin
-    IdentityFile PATH_TO_KEY
+    User {LifeScienceLogin}
+    IdentityFile {PATH_TO_KEY}
     ServerAliveInterval 120
 
-Host NAME_OF_VM
-    HostName 172.16.XXX.XXX
-    IdentityFile PATH_TO_KEY
-    User ubuntu / centos
+Host {NAME_OF_VM}
+    HostName {172.16.XXX.XXX}
+    IdentityFile {PATH_TO_KEY}
+    User {ubuntu / centos}
     ProxyJump denbi-jumphost-01.bihealth.org
-
 ```
 
 #### Setting up a SOCKS proxy
@@ -342,4 +343,4 @@ source openrc.sh
 10.  Use openstack-cli to get information about your project
 ```bash
 openstack server list
-```
+```