## 1. SSH Setup
-1. (Windows only) Install git for windows [https://git-scm.com/download/win](https://git-scm.com/download/win)
+1. (Windows only) Install Git for Windows [https://git-scm.com/download/win](https://git-scm.com/download/win)
1. Choose "64-bit Git for Windows Setup". It does not require admin privileges to install.
1. Hit "Next" a bunch of times to accept the defaults
- 1. The most important things is that "install git bash" and "install OpenSSH" are enabled.
+ 1. The most important things is that "install git bash" and "install OpenSSH" are enabled (this is the default).
1. At the end of the installation, you can launch tick a box to git bash directly.
1. Open "Git Bash" (installed in the "Git" folder of the start menu)
-1. From an open bash shell
+1. (All operating systems) Starting from bash shell (on MacOS or Linux you will open "Terminal")
1. Shell: Run `ssh-keygen`
1. Hit enter to save to a default location
1. You can choose to protect the key with a password, or just hit enter for no password.
- 1. Shell: Look for a message like `Your public key has been saved in /c/Users/MyUsername/.ssh/id_rsa.pub`
- 1. Shell: Run `cat /c/Users/MyUsername/.ssh/id_rsa.pub`
+ 1. Shell: Look for a message like `Your public key has been saved
+ in /c/Users/MyUsername/.ssh/id_rsa.pub` (Windows git bash
+ example, on MacOS or Linux this will probably start with `/Users` or `/home`)
+ 1. Shell: Run `cat /c/Users/MyUsername/.ssh/id_rsa.pub`
1. Shell: Use the pointer to highlight and copy the lines starting
with `ssh-rsa …` up to the next blank line. Right click and
select "Copy"
## 2. VSCode setup
1. Install [Visual Studio Code](https://code.visualstudio.com/) and start it up
-1. Vscode: go to `Extensions` 
- 1. search for `remote development` and install the Remote Development extension pack from Microsoft
-1. Vscode: On the left side bar, choose `Remote explorer`
- 1. In the drop down, choose `SSH targets`
- 1. Click `Add new`
+1. Vscode: On the left sidebar, select `Extensions` 
+ 1. In `Search Extensions in Marketplace` enter "remote development".
+ 1. Choose and install the "Remote Development" extension pack from Microsoft
+1. Vscode: On the left sidebar, choose `Remote Explorer` 
+ 1. At the top of the Remote Explorer panel choose `SSH targets` 
+ 1. Click `Add New` 
1. Enter the `ssh shell…` command line you used in the previous section, step 1.4.1
- 1. Right click the ssh target in the list and select “connect to host in current window`
-1. Vscode: go to `Extensions`
- 1. Search for `benten` and install `CWL (Rabix/Benten)`
- 1. Choose `Install extension on the remote ssh host`
-1. Vscode: On the left side bar, choose `Explorer`
- 1. Select `Clone Repository` and then enter [https://github.com/arvados/arvados-vscode-cwl-training](https://github.com/arvados/arvados-vscode-cwl-training)
- 1. Choose `Open`
-1. Go to Arvados Workbench
- 1. Workbench: In the user menu, select `Current token`
- 1. Vscode: Click on the `Terminal` menu
+ 1. If it asks you `Select SSH configuration file to update` choose the first one in the list.
+ 1. Right click the newly added ssh target in the list and select “connect to host in current window`
+ 1. If it asks `Select platform of the remote host` select `Linux`.
+1. Vscode: On the left sidebar, go back to `Extensions` 
+ 1. Search for "benten", then look for `CWL (Rabix/Benten)` and click `Install`
+ 1. On the information page for `CWL (Rabix/Benten)`
+ 1. If you see a warning `Install the extension on 'SSH: ...' to enable` then click the button `Install in SSH: ...`
+ 1. You should now see a message `Extension is enabled on 'SSH: ...' and disabled locally.`
+1. Vscode: On the left sidebar, choose `Explorer` 
+ 1. Select `Clone Repository` and enter [https://github.com/arvados/arvados-vscode-cwl-training](https://github.com/arvados/arvados-vscode-cwl-training), then click `Open`
+ 1. If asked `Would you like to open the cloned repository?` choose `Open`
+1. Vscode: Click on the `Terminal` menu
1. Vscode: Click `Run Task…`
1. Vscode: Select `Configure Arvados`
- 1. Workbench: Copy the string following `ARVADOS_API_HOST=`
+ 1. Go to Arvados Workbench
+ 1. Workbench: In the user menu, select `Current token`
+ 1. Workbench: Copy the text following `ARVADOS_API_HOST=` to the end of the line
1. Vscode: Paste the string at the `Value for ARVADOS_API_HOST` prompt
- 1. Workbench: Copy the string following `ARVADOS_API_TOKEN=`
+ 1. Workbench: Copy the text following `ARVADOS_API_TOKEN=` to the end of the line
1. Vscode: Paste the string at the `Value for ARVADOS_API_TOKEN` prompt
+ 1. This will create files called `API_HOST` and `API_TOKEN`
## 3. Register & run a workflow
1. Click on the `Terminal` menu
1. Click `Run Task…`
1. Select `Register or update CWL workflow on Arvados Workbench`
+ 1. This will create a file called `WORKFLOW_UUID`
1. Workbench: Go to `+NEW` and select `New project`
1. Enter a name for the project like "Lesson 1"
1. You should arrive at the panel for the new project
1. Click `Run process`
1. This should take you to a panel showing the workflow run status
1. Workbench: workflow run status panel
- 1. Click on the three vertical dots in the top-right corner
+ 1. Wait for the badge in the upper right to say `Completed`
+ 1. In the lower panel, double click on the `echo` workflow step
+ 1. This will take you to the status panel for the `echo` step
+ 1. Click on the three vertical dots in the top-right corner next to `Completed`
1. Choose `Log`
- 1. Under `event type` choose `stdout`
+ 1. This will take you to the log viewer panel
+ 1. Under `Event Type` choose `stdout`
1. You should see your message
## 4. Working with input and output files
1. Click `Run Task…`
1. Select `Register or update CWL workflow on Arvados Workbench`
1. Go to your desktop
- 1. Using a text editor such as notepad, create a file "message.txt"
- 1. Enter a message like "Hello world" and save
+ 1. Right click on the desktop, select `New > Text Document`
+ 1. Name the file `message`
+ 1. Enter a message like "Hello earth" and save
1. Workbench: Go to `+NEW` and select `New project`
1. Enter a name for the project like "Lesson 2"
1. You should arrive at the panel for the new project
1. Arvados workbench: With `Lesson 2` project selected
1. Click on +NEW and select `New collection`
- 1. Call the collection "my message"
+ 1. For Collection Name enter "my message"
1. Drag and drop `message.txt` into the browser
1. Click `Create a collection`
1. The file should be uploaded and then you will be on the collection page
1. Click on the dot menu
1. Choose `Outputs`
1. Right click on `reverse.txt`
- 1. Click on `Download`
- 1. Open the downloaded file. It should have your results.
+ 1. Click on `Open in new tab`
+ 1. The results should be visible in a new browser tab.
## 5. Register a workflow with default inputs
The default value for the `message` parameter will taken from the `lesson3/defaults.yaml` file
+1. Vscode: Click on the `lesson3/main.cwl` file
+ 1. Click on the `Terminal` menu
+ 1. Click `Run Task…`
+ 1. Select `Register or update CWL workflow on Arvados Workbench`
1. Workbench: Go to `+NEW` and select `New project`
1. Enter a name for the project like "Lesson 3"
1. You should arrive at the panel for the new project
1. The `#main/message` parameter will be pre-filled with your default value. You can choose to change it or use the default.
1. Click `Run process`
1. This should take you to the status page for this workflow
+ 1. The greeting will appear in the `Log` of the `echo` task, which
+ can be found the same way as described earlier in section 3.
## 6. Run a workflow without registering it
1. Vscode: In the bottom panel select the `Terminal` tab
1. In the upper right corner of the Terminal tab select `Task - Run CWL Workflow` from the drop-down
1. Look for logging text like `submitted container_request zzzzz-xvhdp-0123456789abcde`
- 1. Highlight and copy the workflow identifier (this the string containing -xvhdp- in the middle)
+ 1. Highlight and copy the workflow identifier (this the string containing `-xvhdp-` in the middle)
1. The results of this run will appear in the terminal when the run completes.
1. Workbench: Paste the workflow identifier into the search box
1. This will take you to the status page for this workflow
+
+
+## Notes
+
+If you need to change something about the environment of the user on
+the remote host (for example, the user has been added to a new unix
+group) you need to restart the vscode server that runs on the remote
+host. Do this in vscode:
+
+ctrl+shift+p: `Remote-SSH: Kill VS Code Server on Host`
+
+This is because the vscode server remains running on the remote host
+even after you disconnect, so exiting/restarting vscode on the desktop
+has no effect.
projects / arvados-vscode-cwl-training.git / blobdiff