To create a new project, go to the Projects dropdown menu and select the "+NEW" button, then select “New project”.
<figure> !{width: 100%}{{ site.baseurl }}/images/wgs-tutorial/image4.png!
-<figcaption> _*Figure 3*: Adding a new project using Arvados Workbench, select the "+NEW" button in the upper left-hand corner and click "New Project"._ </figcaption> </figure>
+<figcaption> _*Figure 3*: Adding a new project using Arvados Workbench, select the "+NEW" button in the upper left-hand corner and click "New project"._ </figcaption> </figure>
Let’s name your project “WGS Processing Tutorial”. You can also add a description of your project by typing in the **Description - optional** field. The universally unique identifier (UUID) of the project can be found in the URL, or by clicking the info button on the upper right-hand corner.
h3. 4a. Interactively Running a Workflow Using Workbench
-Workflows can be registered in Arvados. Registration allows you to share a workflow with other Arvados users, and let’s them run the workflow by clicking the "+ New" button and selecting "Run a workflow" on the Workbench Dashboard or on the command line by specifying the workflow UUID. Default values can be specified for workflow inputs.
+Workflows can be registered in Arvados. Registration allows you to share a workflow with other Arvados users, and let’s them run the workflow by clicking the "+NEW" button and selecting "Run a workflow" on the Workbench Dashboard or on the command line by specifying the workflow UUID. Default values can be specified for workflow inputs.
We have already previously registered the WGS workflow and set default input values for this set of the walkthrough.
Let’s find the registered WGS Processing Workflow and run it interactively in our newly created project.
-# To find the registered workflow, you can search for by searching for the project "WGS Processing Tutorial", owned by "Tutorial projects", in the search box located at the top of the page. From there, select the workflow "WGS processing workflow scattered over samples".
+# To find the registered workflow, in the left-hand navigation bar, select "Public Favorites". That listing will include the "WGS Processing Workflow" project. Open that project, and it will include the workflow "WGS processing workflow scattered over samples". Open that workflow.
# Once you have found the registered workflow, you can run it your project by using the "Run Workflow" button and selecting your project ("WGS Processing Tutorial") that you set up in Section 3a, under *Project where the workflow will run*.
<figure> !{width: 100%}{{ site.baseurl }}/images/wgs-tutorial/image8.png!
<figcaption> _*Figure 7*: This is the page that pops up when you hit "Run Workflow", the input that needs selected is highlighted in yellow._ </figcaption> </figure>
There several logs available, so here is a basic summary of what some of the more commonly used logs contain. Let's first define a few terms that will help us understand what the logs are tracking.
As you may recall, Arvados Crunch manages the running of workflows. A _container request_ is an order sent to Arvados Crunch to perform some computational work. Crunch fulfils a request by either choosing a worker node to execute a container, or finding an identical/equivalent container that has already run. You can use _container request_ or _container_ to distinguish between a work order that is submitted to be run and a work order that is actually running or has been run. So our container request in this case is just the submitted workflow we sent to the Arvados cluster.
+
A _node_ is a compute resource where Arvardos can schedule work. In our case since the Arvados Playground is running on a cloud, our nodes are virtual machines. @arvados-cwl-runner@ (acr) executes CWL workflows by submitting the individual parts to Arvados as containers and crunch-run is an internal component that runs on nodes and executes containers.
* @stderr.txt@
projects / arvados.git / blobdiff