diff --git a/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md b/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md index 423e9741fa7bd4..9c6ac5eb14ac36 100644 --- a/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md +++ b/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md @@ -17,12 +17,12 @@ requirements: - type: "none" title: An SSH key connected to your account - type: "none" - title: Have a basic understanding of how Galaxy works + title: Have a basic understanding of how Galaxy works time_estimation: "30m" level: Introductory key_points: - - With SRC you can start your own Galaxy on-demand instance in a secure environment - - You can log in and use Galaxy via the SRC with your university credentials + - With SRC you can start your own Galaxy on-demand instance in a secure environment + - You can log in and use Galaxy via the SRC with your university credentials contributions: authorship: - mirelaminkova @@ -46,8 +46,11 @@ follow_up_training: topic_name: admin tutorials: - surf-research-cloud-pulsar + +subtopic: cloud tags: - deploying + --- Using Galaxy via the {SRC} allows researchers to start Galaxy instances on-demand 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) @@ -76,7 +79,7 @@ You must have previous experience working with data inside Galaxy. # Starting a Galaxy instance inside SRC step-by-step > Access the SRC -> 1. The first and most important step is to have access to the SURF Research Cloud. +> 1. The first and most important step is to have access to the SURF Research Cloud. > 2. You will need to login to the [portal](https://portal.live.surfresearchcloud.nl). > ![login screen for SURF research cloud](./images/1.png) > @@ -94,7 +97,7 @@ The purpose of the storage is to attach it to your workspace, where you will sav > Create a Storage Volume -> 1. Locate the "Create new storage" option +> 1. Locate the "Create new storage" option > ![top half of the SRC dashboard showing options like create new workspace, storage, or request a new wallet.](./images/4.png) > 2. Click on "Create new". > 3. Select the collaborative organisation you want the storage to be part of. @@ -104,12 +107,12 @@ The purpose of the storage is to attach it to your workspace, where you will sav > {: .tip} > > ![create your storage dashboard showing a selection of providers like surf and aws and azure, and then a selection of storage sizes below ranging from 5GB to 1.5TB](./images/5.png) -> +> > 6. Name your storage however you like and press on submit. > > ![form to provide name and preview what will be created.](./images/6.png) > -> 7. You will be redirected to the main page, where you will be able to track the status of the storage creation. +> 7. You will be redirected to the main page, where you will be able to track the status of the storage creation. > > ![bottom half of home page showing the Storage tab, and a resource named storage-galaxy in state creating.](./images/7.png) {: .hands_on} @@ -130,24 +133,24 @@ Depending on user’s rights, you can create a new workspace for your collaborat > 1. On the right side under the "Workspaces" click on the "Add" button. > > ![dashboard of workspaces showing a single running workspace titled galaxy test tim, and on the right a button to add a new workspace.](./images/8.png) -> -> 2. Then, you will be redirected to a new page, where you must first choose the collaborative organisation in which you want to create your workspace (in case you are a member of multiple organisations). Once chosen, you a new page will be loaded, where you will have access to all available catalog items. +> +> 2. Then, you will be redirected to a new page, where you must first choose the collaborative organisation in which you want to create your workspace (in case you are a member of multiple organisations). Once chosen, you a new page will be loaded, where you will have access to all available catalog items. > > ![Create your workspace screen showing 9 catalog items on the first page with pages more. Visible are Galaxy Pulsar node amongst some docker and ubuntu options.](./images/9.png) -> +> > 3. Use the magnifying glass on the right side of the panel and search for Galaxy. Two catalog items will appear - the Galaxy instance designed for SURF and a Galaxy Pulsar node that can be connected to the instance. Select "Galaxy at SURF". > > ![similar to previous image, but the items described above](./images/10.png) -> -> 4. SURF Research Cloud allows researchers to host their catalog items on different cloud providers. The Galaxy catalog item is currently supported only on the HPC Cloud and for Ubuntu 22.04. On this page, users can select the number of cores and RAM that they want on their machine. More sizes can be added in the future, and on request. Choose wisely and in case you are not certain contact your administrator! +> +> 4. SURF Research Cloud allows researchers to host their catalog items on different cloud providers. The Galaxy catalog item is currently supported only on the HPC Cloud and for Ubuntu 22.04. On this page, users can select the number of cores and RAM that they want on their machine. More sizes can be added in the future, and on request. Choose wisely and in case you are not certain contact your administrator! > > ![workspace creation screen, choose the cloud provider is locked to SURF HPC, flavour is locked to 22.04, and the size options are available from 1GB/8CPU to 60C/750GB Hi-mem](./images/11.png) -> -> 5. Select the storage you have created earlier so it is attached to the new workspace. +> +> 5. Select the storage you have created earlier so it is attached to the new workspace. > > ![create your workspace screen, storage only lists one option named storage-galaxy](./images/12.png) -> -> 6. Lastly, before the workspace is deployed, you need to choose for how long the machine will run. +> +> 6. Lastly, before the workspace is deployed, you need to choose for how long the machine will run. > > > Expiration Date > > The standard life-time of the VM is 5 days. If you need it for longer, this option can be changed once the machine is running. @@ -155,7 +158,7 @@ Depending on user’s rights, you can create a new workspace for your collaborat > > > > This is an incredibly useful feature as it saves you from forgetting to destroy a VM. Especially for GPU nodes it can help you ensure that they disappear after your computation is complete. > {:.tip} -> +> > 7. In this form, you can also select how to name your workspace, add a description (if you want) and specify the hostname. Then, scroll down and submit the workspace creation. > ![almost there, some final details reads the heading. an expiration date is set and galaxy at surf is provided in the name. the hostname is set to galaxyatsurf and the description is blank](./images/13.png) {: .hands_on} diff --git a/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md b/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md index 2459f083a51cd4..0d7c083a56c40f 100644 --- a/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md +++ b/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md @@ -42,6 +42,8 @@ follow_up_training: tutorials: - surf-research-cloud-galaxy subtopic: cloud +tags: + - deploying --- @@ -95,7 +97,7 @@ You should have previous experience working with data inside Galaxy. > > ![workspace creation screen, choose the cloud provider is locked to SURF HPC, flavour is locked to 22.04, and the size options are available from 1GB/8CPU to 60C/750GB Hi-mem](images/surf5.png) > -> 6. Pick a name, it can be anything, it does not matter. Check the expiration date to ensure it is just enough time for your computation and no more. +> 6. Pick a name, it can be anything, it does not matter. Check the expiration date to ensure it is just enough time for your computation and no more. > > > Expiration Date > > The standard life-time of the VM is 5 days. If you need it for longer, this option can be changed once the machine is running. @@ -117,13 +119,13 @@ Once done, the workspace will be created for you. You'll need to wait ~5 minutes ## Using Pulsar on SRC > Access the Information Page -> +> > 1. Once the workspace is up, you'll see an **Access** link: -> +> > ![A small plus button is hovered over which says Add. Below galaxy-test is shown running with a yellow Access button](images/surf3.png) -> +> > 2. Click that will show you a Pulsar information page. This page is running on your pulsar node itself, and is restricted to ensure only authorised members can access the contents. It includes some configuration you will need to copy to your Galaxy node in order to make use of the Pulsar node. -> +> > ![pulsar configuration information page showing an about with admins and metadata like workspace fqdn. Configuration for galaxy is shown below including XML changes](images/surf8.png) {: .hands_on} @@ -131,16 +133,16 @@ This information page should have more than enough information to connect this P > Configuring Galaxy to use SRC Pulsar > 1. Collect the requirements for accessing the Galaxy machine. You will need: -> +> > - your username from the first step > - your SSH key that is associated with your SRAM account -> +> > 2. SSH into your *Galaxy* machine (not pulsar!). -> +> > ``` > ssh -i path/to/your/sram-ssh-key username@galaxy.src-winter-school.src.surf-hosted.nl > ``` -> +> > 3. You will need to `sudo su` to do anything useful. Do that now. > 4. `cd /srv/galaxy/` to move into the directory Galaxy configuration is stored. > 5. The configuration is discussed fully in the Pulsar information, but it will be briefly covered here as well. Generally there are a few steps that must be followed: @@ -150,8 +152,8 @@ This information page should have more than enough information to connect this P > - Some tools should be redirected to this Pulsar > > Here is an example of what those changes *might* look like in your Galaxy node. In this example our pulsar node was called `p20` but that will be different for you. -> -> {% snippet topics/admin/faqs/diffs.md %} +> +> {% snippet topics/admin/faqs/diffs.md %} > > > ```diff @@ -212,9 +214,9 @@ You can find the tool ID from the dropdown at the top right, just to the left of ![url bar and tool interface for the Cut1 tool](./images/id2.png) > An Easy Configuration Option: Send Every Job to Pulsar -> +> > If you are running jobs for a limited period of time, you might consider making this pulsar node the default destination. Remember to use the `remote_...` name of your pulsar node, based on what you copied. Not `remote_p20`. -> +> > ```diff > execution: > - default: docker_dispatch