diff --git a/events/2025-01-28-src.md b/events/2025-01-28-src.md index 60eb9037465329..c5115075340a89 100644 --- a/events/2025-01-28-src.md +++ b/events/2025-01-28-src.md @@ -2,13 +2,15 @@ layout: event # Status of this page, remove these lines when ready -draft: true -status: wip +#draft: true +#status: wip # Description of your event title: Galaxy at SURF Research Cloud workshop description: | - Half-day workshop demonstrating the local Galaxy instance built for users of SURF Research Cloud. + Half-day workshop demonstrating the local Galaxy instance built for users of SURF Research Cloud. + + **Registration**: To sign up for the event, please send an email to [Mirela Minkova](mailto:mirela.minkova@surf.nl?subject=Registering%20SRC%20Galaxy%20Workshop) @@ -79,11 +81,11 @@ program: - name: surf-research-cloud-pulsar topic: admin - time: "14:10 - 14:40" + time: "14:10 - 14:30" - type: custom name: Coffee Break - time: "14:40" + time: "14:30" - name: mapping topic: sequence-analysis time: "14:40 - 15:40" @@ -99,7 +101,10 @@ program: - type: custom name: Borreltje time: "16:30 - 17:00" - +tags: +- admin +- surf +- netherlands --- During the workshop, you will see a short demo and get a chance to test the catalog item yourself. This will be followed by a discussion about your needs as Galaxy researchers, helping us work toward a better future for the Dutch research community. We will conclude the day with drinks and networking with fellow Galaxy NL users. diff --git a/topics/admin/tutorials/cloudbursting/slides.html b/topics/admin/tutorials/cloudbursting/slides.html index 91fc1a718f7959..f5e06ea4a4df7d 100644 --- a/topics/admin/tutorials/cloudbursting/slides.html +++ b/topics/admin/tutorials/cloudbursting/slides.html @@ -3,9 +3,14 @@ logo: assets/images/gat.png title: "Galaxy on the Cloud" -contributors: +contributions: + authorship: - slugger70 + editing: + - hexylena subtopic: cloud + +priority: 0 --- # All these Clouds @@ -84,7 +89,7 @@ * Education grants * Academic: * OpenStack: open source community project - * NeCTAR in Australia, Jetstream in USA, CLIMB in UK, lots of others + * NeCTAR in Australia, Jetstream in USA, CLIMB in UK, SURF in Netherlands, lots of others * Some free for researchers (NeCTAR, CLIMB), some with project grants (Jetstream) ] @@ -129,7 +134,7 @@ * with Galaxy pre-installed * with different sets of tools installed * with access to reference data - * for different clouds (AWS globally, Jetstream, NeCTAR, CLIMB etc.) + * for different clouds (AWS globally, Jetstream, NeCTAR, CLIMB, SURF etc.) * You just need credentials for the cloud you want to "launch" on. * Credentials are generally strings * An access key and a secret key or username and password with project details @@ -282,6 +287,13 @@ ... ``` + +--- + +# CloudMan Galaxy + +* Configured for Slurm out of the box + ``` ini # COMPUTE NODES NodeName=master NodeAddr=45.113.232.91 CPUs=15 RealMemory=64431 Weight=10 State=UNKNOWN diff --git a/topics/admin/tutorials/k8s-managing-galaxy/tutorial.md b/topics/admin/tutorials/k8s-managing-galaxy/tutorial.md index 600af2747835ea..8a42c3155212d9 100644 --- a/topics/admin/tutorials/k8s-managing-galaxy/tutorial.md +++ b/topics/admin/tutorials/k8s-managing-galaxy/tutorial.md @@ -32,7 +32,7 @@ requirements: topic_name: admin tutorials: - k8s-deploying-galaxy -priority: 1 +priority: 3 --- # Managing Galaxy on Kubernetes diff --git a/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md b/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md index 9c6ac5eb14ac36..9ea5b1e4582a6f 100644 --- a/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md +++ b/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md @@ -31,6 +31,8 @@ contributions: funding: - surf +priority: 10 + edam_ontology: - topic_0605 # Informatics - topic_3071 # Data Management diff --git a/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md b/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md index 0d7c083a56c40f..f276dd70a3d317 100644 --- a/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md +++ b/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md @@ -7,7 +7,12 @@ questions: - How do I start a Pulsar instance on SURF Research Cloud? - How do I connect to Pulsar? objectives: - - Be able to attach a Pulsar node to Galaxy and use interactive tools + - Be able to attach a Pulsar node to Galaxy + - Send jobs to Pulsar +key_points: + - With SRC you can start your own Pulsar on-demand instance in a secure environment. + - The Pulsar node is publicly accessible for a Galaxy with the credentials to use. + - You can send jobs to a Pulsar node from either a Galaxy instance running on SRC, or even inside your own network. requirements: - type: "none" title: Access to the SURF Research Cloud @@ -26,6 +31,8 @@ contributions: funding: - surf +priority: 11 + edam_ontology: - topic_0605 # Informatics - topic_3071 # Data Management @@ -49,9 +56,14 @@ tags: Using Pulsar via the {SRC} allows researchers to start Pulsar instances on-demand to expand their computational resources and even access GPUs to help and analyze their data in a secure environment following the {GDPR}. -The instance provides secure authentication, where users must have a SURF Research account prior to this tutorial, have set the {SRAM} authentication method, and connect an SSH key to their accounts. In case you are not familiar with {SRC} and need help in setting up your accounts, please follow the instructions on the [SURF Knowledge Base](https://servicedesk.surf.nl/wiki/display/WIKI/SURF+Research+Cloud) +There are two main use cases we envision this role being useful for: + +Saving costs on SRC +: Maybe you're already running Galaxy in SRC, but you don't want to run a GPU node because it is very expensive. By using the SRC Pulsar Catalog Item, you can launch a node to do computations and then shut it down when you're done, saving money. Pulsar instances can be started and stopped on demand, depending on personal cases and requirements, giving you a lot of freedom! + +Accessing a GPU from a local (in UMC/hospital Galaxy) +: If you do not have a GPU easily available within your institute, it may be attractive to send jobs securely to SRC, by launching a Pulsar node in SRC and attaching it to your institute's Galaxy instance. -Pulsar instances can be started and stopped on demand, depending on personal cases and requirements. Inside the SRC members should have access to all publicly available catalog items. If you are not able to create a catalog item, please [contact SURF servicedesk](mailto:servicedesk@surf.nl). > > @@ -62,6 +74,10 @@ Pulsar instances can be started and stopped on demand, depending on personal cas # Prerequisites +The instance provides secure authentication, where users must have a SURF Research account prior to this tutorial, have set the {SRAM} authentication method, and connect an SSH key to their accounts. In case you are not familiar with {SRC} and need help in setting up your accounts, please follow the instructions on the [SURF Knowledge Base](https://servicedesk.surf.nl/wiki/display/WIKI/SURF+Research+Cloud) + +Inside the SRC members should have access to all publicly available catalog items. If you are not able to create a catalog item, please [contact SURF servicedesk](mailto:servicedesk@surf.nl). + This tutorial assumes you are member of a {CO} in {SRAM} that has access to {SRC} and a wallet with budget in SRC with enough sources to create Galaxy and Pulsar catalog items. (For more information please refer to the [SURF Knowledge Base](https://servicedesk.surf.nl/wiki/display/WIKI/Budgets%2C+wallets%2C+contracts). You should have previous experience working with data inside Galaxy. @@ -229,4 +245,15 @@ You can find the tool ID from the dropdown at the top right, just to the left of With that, you're done, and for the length of time your node is running, your chosen tools (or everything) will be executed on that Pulsar node with more memory and CPU than the Galaxy host, and maybe a GPU as well! +> Launch a Job on Pulsar +> 1. Login to your Galaxy +> 2. Run one of the tools you have decided to send to Pulsar +> 3. On the pulsar machine, you can check that it runs by following the logs: +> +> ```bash +> sudo journalctl -fu pulsar +> ``` +> +{: .hands_on} + Congratulations on launching Pulsar in SRC! 🌌 diff --git a/topics/admin/tutorials/terraform/slides.html b/topics/admin/tutorials/terraform/slides.html index 31238267ad5cce..387062a5b41328 100644 --- a/topics/admin/tutorials/terraform/slides.html +++ b/topics/admin/tutorials/terraform/slides.html @@ -17,6 +17,8 @@ subtopic: cloud contributors: - hexylena + +priority: 30 --- ### Why Terraform diff --git a/topics/admin/tutorials/terraform/tutorial.md b/topics/admin/tutorials/terraform/tutorial.md index 5e0340fce1e5ba..36e6e04318db18 100644 --- a/topics/admin/tutorials/terraform/tutorial.md +++ b/topics/admin/tutorials/terraform/tutorial.md @@ -23,6 +23,8 @@ tags: - deploying - cloud priority: 3 + +priority: 30 --- # Overview diff --git a/topics/admin/tutorials/wireguard-headscale/tutorial.md b/topics/admin/tutorials/wireguard-headscale/tutorial.md index c94c99bab6a688..0400a169419e0b 100644 --- a/topics/admin/tutorials/wireguard-headscale/tutorial.md +++ b/topics/admin/tutorials/wireguard-headscale/tutorial.md @@ -31,6 +31,10 @@ subtopic: cloud tags: - wireguard - networking +edam_ontology: +- topic_3263 # data security +- topic_3372 # software engineering +priority: 20 --- [Tailscale](https://tailscale.com/) makes secure networking easy, it really is like magic. If you've used wireguard before, you know it takes a bit to setup and some configuration if you need to do anything fancy. diff --git a/topics/admin/tutorials/wireguard/tutorial.md b/topics/admin/tutorials/wireguard/tutorial.md index 1d78e2b492e771..6d8ef996855035 100644 --- a/topics/admin/tutorials/wireguard/tutorial.md +++ b/topics/admin/tutorials/wireguard/tutorial.md @@ -26,6 +26,7 @@ subtopic: cloud tags: - wireguard - networking +priority: 20 --- In this tutorial we will briefly cover what [Wireguard](https://www.wireguard.com/) is and how you can leverage it for your needs. This will not make you an expert on Wireguard but will give you the tools you need in order to setup a local Wireguard network.