diff --git a/config.yml b/config.yml index 4612fc28..655f4c4a 100644 --- a/config.yml +++ b/config.yml @@ -29,21 +29,24 @@ 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 + fallback_to_build_date: true - htmlproofer: - enabled: !ENV [ENABLED_HTMLPROOFER,False] - raise_error: True + enabled: !ENV [ ENABLED_HTMLPROOFER,False ] + raise_error_after_finish: True raise_error_excludes: - -1: ["https://cloud.denbi.de/portal/webapp/#/userinfo","http://169.254.169.254","https://login.elixir-czech.org/oidc/","https://spreg-legacy.aai.elixir-czech.org/spreg/auth/requests/new","https://spreg-legacy.aai.elixir-czech.org/spreg/auth/facilities/myServices","http://BIBIGRID_MASTER/ganglia"] - 400: ["http://169.254.169.254"] - 500: ["https://cloud.denbi.de/register", "https://signup.aai.lifescience-ri.eu/fed/registrar/?vo=elixir_test"] + -1: [ "https://cloud.denbi.de/portal/webapp/#/userinfo","http://169.254.169.254","https://login.elixir-czech.org/oidc/","https://spreg-legacy.aai.elixir-czech.org/spreg/auth/requests/new","https://spreg-legacy.aai.elixir-czech.org/spreg/auth/facilities/myServices","http://BIBIGRID_MASTER/ganglia" ] + 400: [ "http://169.254.169.254" ] + 403: [ "https://s3.denbi.uni-tuebingen.de" ] + 500: [ "https://cloud.denbi.de/register", "https://signup.aai.lifescience-ri.eu/fed/registrar/?vo=elixir_test" ] + 504: [ "https://cloud.denbi.de/about/credits-calculator/", "https://packages.ubuntu.com/","https://denbi-cloud.bihealth.org","http://apt-cache.bi.denbi.de:9999","http://129.70.51.2:9999","https://cloud.denbi.dkfz-heidelberg.de","https://denbi-cloud.bioquant.uni-heidelberg.de","https://denbi-cloud.bioquant.uni-heidelberg.de" ] + markdown_extensions: - abbr - attr_list @@ -103,64 +106,64 @@ 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 - simplevm_wiki_link: !ENV [SIMPLE_VM_WIKI_LINK, 'https://simplevm.denbi.de/wiki/'] + name: de.NBI on Wikipedia + simplevm_wiki_link: !ENV [ SIMPLE_VM_WIKI_LINK, 'https://simplevm.denbi.de/wiki/' ] nav: - - 'Home' : index.md - - 'Registration' : registration.md + - 'Home': index.md + - 'Registration': registration.md - 'Citation and publication': citation_and_publication.md - - 'Portal' : - - 'Allocation': portal/allocation.md - - 'Resource/Lifetime Modifications': portal/modification.md - - 'Project Termination' : portal/termination.md - - 'Project Overview': portal/project_overview.md - - 'Profile Page': portal/user_information.md - - 'Using Vault': portal/vault_user.md - - 'Cloud Credits': portal/credits.md - - 'Personal Data': portal/personal_data.md + - 'Portal': + - 'Allocation': portal/allocation.md + - 'Resource/Lifetime Modifications': portal/modification.md + - 'Project Termination': portal/termination.md + - 'Project Overview': portal/project_overview.md + - 'Profile Page': portal/user_information.md + - 'Using Vault': portal/vault_user.md + - 'Cloud Credits': portal/credits.md + - 'Personal Data': portal/personal_data.md - 'Simple VM': - simple_vm/index.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 + - '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 - - 'News management': cloud_admin/news_management.md - - 'Vault management': cloud_admin/vault_admin.md + - '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 + - 'News management': cloud_admin/news_management.md + - 'Vault management': cloud_admin/vault_admin.md diff --git a/wiki/FAQ.md b/wiki/FAQ.md index ccd0e33a..42ccef63 100644 --- a/wiki/FAQ.md +++ b/wiki/FAQ.md @@ -23,7 +23,7 @@ If this does not bring the desired success, the reasons can be manifold. Make sure that you use the correct SSH key! If you have changed your SSH key in the portal since creating the machine, it will not be automatically changed on this machine. The connection to this VM still requires the key that was set at the time of creation. The private key is always used to connect to the machine. -You can find more about SSH keys [here](./simple_vm/keypairs.md#ssh-keys-and-sharing-access). +You can find more about SSH keys [here]({{extra.simplevm_wiki_link}simple_vm/keypairs/). Maintenance may be performed at the site where your machines are running. Occasionally, malfunctions also occur during regular service. Check your project site's [Facility News](https://cloud.denbi.de/news/facility-news/) page - downtimes are usually announced on this page. diff --git a/wiki/Tutorials/Elixir_AAI/Elixir_AAI.md b/wiki/Tutorials/Elixir_AAI/Elixir_AAI.md index 17f5167f..55652076 100644 --- a/wiki/Tutorials/Elixir_AAI/Elixir_AAI.md +++ b/wiki/Tutorials/Elixir_AAI/Elixir_AAI.md @@ -12,7 +12,7 @@ In this section you can see an illustration of our finished architecture. ![](Goal_Architecture.png) ​ ## What do we need before we start? -1. We need a running virtual instance that is accessible from the web. You can find a tutorial on how to create one in the de.NBI wiki: . The hardware specs we used for this project are: OS: Ubuntu 18.04 LTS; RAM: 4GB; HDD: 20 GB. +1. We need a running virtual instance that is accessible from the web. You can find a tutorial on how to create one in the de.NBI SimpleVM wiki: . The hardware specs we used for this project are: OS: Ubuntu 18.04 LTS; RAM: 4GB; HDD: 20 GB. 2. You need a registered Elixir client. You can register here: . After the registration you can access your personal profile via this link: . Here you can find e.g . your personal Elixir client ID. 3. Create an Elixir service you will use to authenticate at the reverse proxy later on. This service can be registered here: . 4. To be able to access the services in the test environment, you need to register to a special "virtual organization" representing this environment. You can register at: . Note: The membership in this VO is valid for one month and has to be extended to be able to use the test environment in the future. diff --git a/wiki/Tutorials/ObjectStorage/index.md b/wiki/Tutorials/ObjectStorage/index.md index ca77a4ce..fd45fc3c 100644 --- a/wiki/Tutorials/ObjectStorage/index.md +++ b/wiki/Tutorials/ObjectStorage/index.md @@ -18,7 +18,7 @@ A caveat on object stores is the possible higher network latency between the sto ### Object storage access Depending on the cloud site the object storage is based on different storage backends. It can be accessed using -the [https://docs.aws.amazon.com/AmazonS3/latest/API/Welcome.html](S3-API). SThese APIs differ in +the [S3-API](https://docs.aws.amazon.com/AmazonS3/latest/API/Welcome.html). These APIs differ in their terminology, capabilities and respective tools: Objects are stored in containers (swift) or buckets (s3). Access is controlled via access control lists (s3 and swift) or via policies (only s3). diff --git a/wiki/Tutorials/Persistent_SSH_Sessions/index.md b/wiki/Tutorials/Persistent_SSH_Sessions/index.md index 1e3f6dcc..cf93c5a8 100644 --- a/wiki/Tutorials/Persistent_SSH_Sessions/index.md +++ b/wiki/Tutorials/Persistent_SSH_Sessions/index.md @@ -80,7 +80,7 @@ This way you can easily create persistent sessions with screen that are independ - Screen Cheatsheet - https://quickref.me/screen -- Manpage: [Screen](https://linux.die.net/man/1/screen) or +- Manpage: ```bash $ man screen diff --git a/wiki/Tutorials/RStudio_Server/index.md b/wiki/Tutorials/RStudio_Server/index.md index 0bb29229..725ca940 100644 --- a/wiki/Tutorials/RStudio_Server/index.md +++ b/wiki/Tutorials/RStudio_Server/index.md @@ -165,4 +165,4 @@ sudo apt-get install libcurl4-gnutls-dev libssl-dev libcurl4-openssl-dev libxml2 After the installation of these packages, try to re-install the R packages in RStudio Server. Hopefully the error vanished now! ## 6. Further Reading -For more information on RStudio and the RStudio Server please have a look at their documentation at ([https://support.rstudio.com/hc/en-us/categories/200035113-Documentation](https://support.rstudio.com/hc/en-us/categories/200035113-Documentation)) +For more information on RStudio and the RStudio Server please have a look at their documentation at ([https://docs.posit.co/ide/user/](https://docs.posit.co/ide/user/)) diff --git a/wiki/Tutorials/X2GO/x2go.md b/wiki/Tutorials/X2GO/x2go.md deleted file mode 100644 index 1d288268..00000000 --- a/wiki/Tutorials/X2GO/x2go.md +++ /dev/null @@ -1,68 +0,0 @@ -# X2Go - -!!! Deprecated - We recommend to use [Apache Guacamole](../../simple_vm/customization.md#apache-guacamole) instead. This applies only for our SimpleVM project type and does not affect OpenStack. We offer to install it on your virtual machines with a single click while starting up. It allows you to use the user interface of your machine at any time without an additional client via your favourite web browser - no further configuration on your part is necessary. Please have in mind, that the usage of Guacamole is only possible, when selected during creation of a virtual machine! Consider our [Backup article](../../simple_vm/backup.md) to use your existing data and tools on a new machine. - -X2Go allows you to start your own desktop in the de.NBI Cloud which you can access from any operating system (Windows, Linux, MacOS). - -## Installation - -#### First Steps - -In order to install X2Go, connect to the corresponding machine first. -Make sure, that the `software-properties-common` package is installed. On Ubuntu 16.04 and higher the package should already have the newest version. - -Run the following commands to install the X2Go-server on your machine. -> sudo add-apt-repository ppa:x2go/stable - -> sudo apt-get update - -> sudo apt-get install x2goserver x2goserver-xsession - -In the next step, install a desktop binding for the desktop environment you like. -In this tutorial we will use `LXDE`, but you can find bindings and install instructions for several environments [here](https://wiki.x2go.org/doku.php/wiki:advanced:desktopbindings). - -For LXDE, run the following commands: -> sudo apt install aptitude - -> sudo aptitude install x2golxdebindings - -#### Export key in OpenSSH format for X2GO (Windows only) -To connect to a machine with X2GO you have to export your private key in openssh format. To achieve this first load your private key into puttygen. - -![X2Go Client](../../portal/img/putty_private.png) - -Then click Conversions and choose Export OpenSSH Key. Afterwards save this file on your computer. This file will be needed when you want to establish a connection to a machine with the X2GO client. - -![SSH_export](../../portal/img/putty_export.png) - -## Usage - -#### Connect to X2GO machine - -To connect to X2Go, you need a client e.g the X2Go client you can find [here](https://wiki.x2go.org/doku.php/download:start). -As a macOS user make sure that [XQuartz](https://www.xquartz.org) is installed. - -When you start the X2Go client, you need to enter the session preferences first. -Choose any name you like for the session. -The following data, most of which can be found on the details page of the VM running X2Go, is of relevance: -- The IP of the machine -- The port of the machine -- The path of your private key. The key can be easily selected via the user interface -- The username for the connection to the machine. By default this is `ubuntu` - -![X2Go Information](../../portal/img/x2go_session.png) - - -Select your private key, which you use to connect to the machine. -For the session type select `LXDE` or any other desktop environment you have installed in advance. -The IP is the first marked information on the previous picture. The port is the second marked information. -This information can be found as described on the details page of your VM. - -After you have saved the session preferences, you can now select the session and connect to the machine. - -![X2Go Client](../../portal/img/x2go_client.png) - - - - diff --git a/wiki/Tutorials/index.md b/wiki/Tutorials/index.md index db6787a2..43001bae 100644 --- a/wiki/Tutorials/index.md +++ b/wiki/Tutorials/index.md @@ -1,7 +1,7 @@ # Tutorials Welcome to the tutorials section! Explore the guides below to enhance your knowledge and skills in various topics. -SimpleVM-specific Tutorials can be found in the SimpleVM-Wiki [tutorial section]({{extra.simplevm_wiki_link}}/Tutorials) +SimpleVM-specific Tutorials can be found in the SimpleVM-Wiki [tutorial section]({{extra.simplevm_wiki_link}}Tutorials/) - [Access de.NBI Virtual Machines from Windows 10](Win10_SSH/index.md) @@ -22,4 +22,3 @@ SimpleVM-specific Tutorials can be found in the SimpleVM-Wiki [tutorial section] - [Persistent SSH Sessions](Persistent_SSH_Sessions/index.md) - [Theia Web IDE](TheiaIde/index.md) - [UserData](UserData/index.md) -- [Using X2GO](X2GO/x2go.md) diff --git a/wiki/portal/user_information.md b/wiki/portal/user_information.md index 488c51bc..f55cdec3 100644 --- a/wiki/portal/user_information.md +++ b/wiki/portal/user_information.md @@ -32,8 +32,8 @@ https://signup.aai.lifescience-ri.eu/fed/registrar/?vo=anonymize ### SSH Key ![setcopypublickey](img/profile_page.png) -You have the possibility to view, copy and deposit your public ssh key. An uploaded public key is required for starting machines. -Read more about it [here](../simple_vm/new_instance.md#3-grant-access-for-project-members). + +You have the possibility to view, copy and deposit your public ssh key. If you don't know how to generate a ssh key, you can read the [instructions](../quickstart.md#generate-ssh-keys) on our quickstart page. Alternatively you are also able to have a ECDSA key generated for you. Click on the `Generate Key` button and read and confirm the notification.