Copy pipeline from Curoverse cloud

This tutorial describes how to find and copy a publicly shared pipeline from Curoverse cloud. Please note that you can use similar steps to copy any template you can access from Curoverse cloud to your cluster.

Access a public pipeline in Curoverse cloud using Workbench

Curoverse cloud provides access to some public data, which can be used to experience Arvados in action. Let’s access a public pipeline and copy it to your cluster, so that you can run it in your environment.

Start by visiting the Curoverse public projects page. This page lists all the publicly accessible projects in this arvados installation. Click on one of these projects to open it. We will use lobSTR v.3 (Public) as the example in this tutorial.

Once in the lobSTR v.3 (Public) project, click on the Pipeline templates tab. In the pipeline templates tab, you will see a template named lobSTR v.3. Click on the Show button to the left of this name. This will take to you to the lobSTR v.3 template page.

Once in this page, you can take the uuid of this template from the address bar, which is qr1hi-p5p6p-9pkaxt6qjnkxhhu. Next, we will copy this template to your Arvados instance.

Copying a pipeline template from Curoverse cloud to your cluster

As described above, navigate to the publicly shared pipeline template lobSTR v.3 using Curoverse Workbench. We will now copy this template with uuid qr1hi-p5p6p-9pkaxt6qjnkxhhu to your cluster.

Note:

This tutorial assumes that you are logged into an Arvados VM instance (instructions for Webshell or Unix or Windows) or you have installed the Arvados Command line SDK and Python SDK on your workstation and have a working environment.

We will use the Arvados arv-copy command to copy this template to your cluster. In order to use arv-copy, first you need to setup the source and destination cluster configuration files. Here, qr1hi would be the source cluster and your Arvados instance would be the dst_cluster.

During this setup, if you have an account in Curoverse cloud, you can use your access token to create the source configuration file. If you do not have an account in Curoverse cloud, you can use the anonymous access token for the source cluster configuration.

Configuring source and destination setup files using anonymous access token

Configure the source and destination clusters as described in the Using arv-copy tutorial in user guide, while using 5vqmz9mik2ou2k9objb8pnyce8t97p6vocyaouqo3qalvpmjs5 as the API token for source configuration.

~$ cd ~/.config/arvados
~$ echo "ARVADOS_API_HOST=qr1hi.arvadosapi.com" >> qr1hi.conf
~$ echo "ARVADOS_API_TOKEN=5vqmz9mik2ou2k9objb8pnyce8t97p6vocyaouqo3qalvpmjs5" >> qr1hi.conf

You can now copy the pipeline template from qr1hi to your cluster. Replace dst_cluster with the uuid_prefix of your cluster.

~$  arv-copy --no-recursive --src qr1hi --dst dst_cluster qr1hi-p5p6p-9pkaxt6qjnkxhhu

Note: When you are using anonymous access token to copy the template, you will not be able to do a recursive copy since you will not be able to provide the dst-git-repo parameter. In order to perform a recursive copy of the template, you would need to use the Arvados API token from your account as explained in the using your token section below.

Configuring source and destination setup files using personal access token

If you already have an account in Curoverse cloud, you can follow the instructions in the Using arv-copy user guide to get your Current token for source and destination clusters, and use them to create the source qr1hi.conf and dst_cluster.conf configuration files.

You can now copy the pipeline template from qr1hi to your cluster with or without recursion. Replace dst_cluster with the uuid_prefix of your cluster.

Non-recursive copy:

~$  arv-copy --no-recursive --src qr1hi --dst dst_cluster qr1hi-p5p6p-9pkaxt6qjnkxhhu

Recursive copy:

~$ arv-copy --src qr1hi --dst dst_cluster --dst-git-repo $USER/tutorial qr1hi-p5p6p-9pkaxt6qjnkxhhu


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The content of this documentation is licensed under the Creative Commons Attribution-Share Alike 3.0 United States licence.
Code samples in this documentation are licensed under the Apache License, Version 2.0.