We have already previously registered the WGS workflow and set default input values for this set of the walkthrough.
-Let’s find the the registered WGS Processing Workflow and run it interactively in our newly created project.
+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 it in the search box located in the top right corner of the Arvados Workbench by looking for the name “WGS Processing Workflow”.
# Once you have found the registered workflow, you can run it your project by using the <span class="btn btn-sm btn-primary" >Run this workflow..</span> button and selecting your project ("WGS Processing Tutorial") that you set up in Section 3a.
Arvados provides a virtual machine which has all the necessary client-side libraries installed to submit to your Arvados cluster using the command line. Webshell gives you access to an Arvados Virtual Machine (VM) from your browser with no additional setup. You can access webshell through the Arvados Workbench. It is the easiest way to try out submitting a workflow to Arvados via the command line.
-To get access to webshell on the Arvados Playground, you need to contact a Curii Arvados Playground Administrator to get access to an Arvados shell node by emailing "info@curii.com.":mailto:info@curii.com
+New users are playground are automatically given access to a shell account.
-Once you receive an email letting you know your access has been set up and you should be able to access the shell virtual machine. You can follow the instructions here to access the machine using the browser (also known as using webshell):
+_Note_: the shell accounts are created on an interval and it may take up to two minutes from your initial log in before the shell account is created.
+
+You can follow the instructions here to access the machine using the browser (also known as using webshell):
* "Accessing an Arvados VM with Webshell":{{ site.baseurl }}/user/getting_started/vm-login-with-webshell.html
Arvados also allows you to ssh into the shell machine and other hosted VMs instead of using the webshell capabilities. However this tutorial does not cover that option in-depth. If you like to explore it on your own, you can allow the instructions in the documentation here:
** Contains about resource consumption (RAM, cpu, disk, network) on the node while it was running
This is different from the log crunchstat.txt because it includes resource consumption of Arvados components that run on the node outside the container such as crunch-run and other processes related to the Keep file system.
-For the highest level logs, the logs are tracking the container that ran the @arvados-cwl-runner@ process which you can think of as the “mastermind” behind tracking which parts of the CWL workflow need to be run when, which have been run already, what order they need to be run, which can be run simultaneously, and so forth and then sending out the related container requests. Each step then has their own logs related to containers running a CWL step of the workflow including a log of standard error that contains the standard error of the code run in that CWL step. Those logs can be found by expanding the steps and clicking on the link to the log collection.
+For the highest level logs, the logs are tracking the container that ran the @arvados-cwl-runner@ process which you can think of as the “workflow runner”. It tracks which parts of the CWL workflow need to be run when, which have been run already, what order they need to be run, which can be run simultaneously, and so forth and then creates the necessary container requests. Each step has its own logs related to containers running a CWL step of the workflow including a log of standard error that contains the standard error of the code run in that CWL step. Those logs can be found by expanding the steps and clicking on the link to the log collection.
-Let’s take a peek at a few of these logs to get you more familiar with them. First, we can look at the @stderr.txt@ of the highest level process. Again recall this should be of the “mastermind” @arvados-cwl-runner@ process. You can click on the log to download it to your local machine, and when you look at the contents - you should see something like the following...
+Let’s take a peek at a few of these logs to get you more familiar with them. First, we can look at the @stderr.txt@ of the highest level process. Again recall this should be of the “workflow runner” @arvados-cwl-runner@ process. You can click on the log to download it to your local machine, and when you look at the contents - you should see something like the following...
<pre><code>2020-06-22T20:30:04.737703197Z INFO /usr/bin/arvados-cwl-runner 2.0.3, arvados-python-client 2.0.3, cwltool 1.0.20190831161204
2020-06-22T20:30:04.743250012Z INFO Resolved '/var/lib/cwl/workflow.json#main' to 'file:///var/lib/cwl/workflow.json#main'
projects / arvados.git / blobdiff