These lessons give step by step instructions for using Visual Studio
-Code to develop CWL workflows on Arvados.
-
-1. Install & set up ssh client on Windows
-1. Install vscode and relevant extensions
-1. Use vscode to connect to an arvados shell node for development
-1. Create an simple command line tool, run it, and view the log
-1. Upload input, create a command line tool to process it, and view the output
-
-# Windows SSH Setup
-
-Linux and MacOS users can skip this step.
-
-1. Install git for windows https://git-scm.com/download/win
-1. Open git bash
-1. Run “ssh-keygen”
-1. Look for “Your public key has been saved in /c/Users/MyUsername/.ssh/id_rsa.pub”
-1. Run “cat /c/Users/MyUsername/.ssh/id_rsa.pub”
-1. Copy the lines starting with “ssh-rsa …”
-1. Open Arvados workbench
-1. Go to “SSH keys” in the user menu
-1. Click + Add new ssh key
-1. Paste the key into “Public key” and enter something for “name”
-1. At the git bash command line, run “ssh shell…” and say “yes” if it asks “do you want to continue connecting”
-1. You should be logged into the Arvados shell node.
-1. Log out by typing “exit”
-
-# VSCode setup
-
-1. Install vscode 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. Enter the “ssh shell…” command line you used in step 1(j)
- 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”
- 1. Choose “Open”
+Code (abbreviated "vscode") to develop CWL workflows on Arvados.
+
+1. Set up SSH
+1. Install vscode and necessary extensions, then use vscode to connect to an Arvados shell node for development
+1. Register a workflow, run it on workbench, and view the log
+1. Upload input, run a workflow on it, and view the output
+1. Register a workflow with default inputs
+1. Run a workflow without registering it
+
+## 1. SSH Setup
+
+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. 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. 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: Use the pointer to highlight and copy the lines starting
+ with `ssh-rsa …` up to the next blank line. Right click and
+ select "Copy"
+1. Open Arvados workbench 2. If necessary, go to the user menu and
+ select "Go to Workbench 2"
+ 1. Workbench: Go to `SSH keys` in the user menu
+ 1. Workbench:Click `+Add new ssh key`
+ 1. Workbench: Paste the key into `Public key` and enter something for `name`
+ 1. Workbench: Go to `Virtual Machines` in the user menu
+ 1. Workbench: Highlight and copy the value in in the `Command line` column.
+1. At the git bash command line
+ 1. Shell: paste the `ssh shell…` command line you got from workbench.
+ 1. Shell: type "yes" if it asks `Are you sure you want to continue connecting`.
+ 1. Note: it can take up to two minutes for the SSH key to be copied to
+ the shell node. If you get "Permission denied" the first time, wait 60
+ seconds and try again.
+ 1. Shell: You should now be logged into the Arvados shell node.
+ 1. Shell: Log out by typing `exit`
+
+## 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. 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. Vscode: Click “Run Task…”
- 1. Vscode: Select “Configure Arvados”
- 1. Workbench: Copy the string following “ARVADOS_API_HOST=”
- 1. Vscode: Paste the string at the “Value for ARVADOS_API_HOST” prompt
- 1. Workbench: Copy the string following “ARVADOS_API_TOKEN=”
- 1. Vscode: Paste the string at the “Value for ARVADOS_API_TOKEN” prompt
-
-# Register & run a workflow
-
-1. Vscode: Click on the “lesson1/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 1”
+ 1. Workbench: In the user menu, select `Current token`
+ 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. Vscode: Paste the string at the `Value for ARVADOS_API_HOST` prompt
+ 1. Workbench: Copy the string following `ARVADOS_API_TOKEN=`
+ 1. Vscode: Paste the string at the `Value for ARVADOS_API_TOKEN` prompt
+
+## 3. Register & run a workflow
+
+1. Vscode: Click on the `lesson1/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 1"
1. You should arrive at the panel for the new project
-1. Workbench: With “Lesson 1” selected
- 1. Click on “+NEW” and select “Run a process”
- 1. Select “CWL training lesson 1” from the list and click “Next”
- 1. Enter a name for this run like “First training run”
- 1. Enter a message (under “#main/message”) like “Hello world”
- 1. Click “Run process”
+1. Workbench: With `Lesson 1` selected
+ 1. Click on `+NEW` and select `Run a process`
+ 1. Select `CWL training lesson 1` from the list and click `Next`
+ 1. Enter a name for this run like `First training run`
+ 1. Enter a message (under `#main/message`) like "Hello world"
+ 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. Choose “Log”
- 1. Under “event type” choose “stdout”
+ 1. Choose `Log`
+ 1. Under `event type` choose `stdout`
1. You should see your message
-# Working with input and output files
+## 4. Working with input and output files
-1. Vscode: Click on the “lesson2/main.cwl” file
- 1. Click on the “Terminal” menu
- 1. Click “Run Task…”
- 1. Select “Register or update CWL workflow on Arvados Workbench”
+1. Vscode: Click on the `lesson2/main.cwl` file
+ 1. Click on the `Terminal` menu
+ 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. Workbench: Go to “+NEW” and select “New project”
- 1. Enter a name for the project like “Lesson 2”
+ 1. Using a text editor such as notepad, create a file "message.txt"
+ 1. Enter a message like "Hello world" 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. Drag and drop “message.txt” into the browser
- 1. Click “Create a collection”
+1. Arvados workbench: With `Lesson 2` project selected
+ 1. Click on +NEW and select `New collection`
+ 1. Call the collection "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. Workbench: Select the “Lesson 2” project
- 1. Click on “+NEW” and select “Run a process”
- 1. Select “CWL training lesson 2” from the list and click “Next”
- 1. Enter a name for this run like “Second training run”
- 1. Click on “#main/message”
+1. Workbench: Select the `Lesson 2` project
+ 1. Click on `+NEW` and select `Run a process`
+ 1. Select `CWL training lesson 2` from the list and click `Next`
+ 1. Enter a name for this run like "Second training run"
+ 1. Click on `#main/message`
1. A selection dialog box will appear
- 1. Navigate to the collection you created in step (13) and choose “message.txt”
- 1. Click “Run process”
+ 1. Navigate to the collection you created in step (4.4.4) and choose `message.txt`
+ 1. Click `Run process`
1. This should take you to a panel showing the workflow run status
1. Workbench: workflow run status panel
1. Wait for the process to complete
1. Click on the dot menu
- 1. Choose “Outputs”
- 1. Right click on “reverse.txt”
- 1. Click on “Download”
+ 1. Choose `Outputs`
+ 1. Right click on `reverse.txt`
+ 1. Click on `Download`
1. Open the downloaded file. It should have your results.
-# Register a workflow with default inputs
+## 5. Register a workflow with default inputs
-The default value for the “message” parameter will taken from the “lesson3/defaults.yaml” file
+The default value for the `message` parameter will taken from the `lesson3/defaults.yaml` file
-1. Workbench: Go to “+NEW” and select “New project”
- 1. Enter a name for the project like “Lesson 3”
+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. Workbench: With “Lesson 3” selected
- 1. Click on “+NEW” and select “Run a process”
- 1. Select “CWL training lesson 3” from the list and click “Next”
- 1. Enter a name for this run like “Third training run”
- 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. Workbench: With `Lesson 3` selected
+ 1. Click on `+NEW` and select `Run a process`
+ 1. Select `CWL training lesson 3` from the list and click `Next`
+ 1. Enter a name for this run like "Third training run"
+ 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
-# Run a workflow without registering it
+## 6. Run a workflow without registering it
-The “message” parameter will be taken from the file “lesson4/main-input.yaml”. This is useful during development.
+The `message` parameter will be taken from the file `lesson4/main-input.yaml`. This is useful during development.
-1. Workbench: Go to “+NEW” and select “New project”
- 1. Enter a name for the project like “Lesson 4”
+1. Workbench: Go to `+NEW` and select `New project`
+ 1. Enter a name for the project like "Lesson 4"
1. You should arrive at the panel for the new project
- 1. Click on “Additional info” in the upper right to expand the “info” panel
- 1. Under “Project UUID” click the “Copy to clipboard” button
-1. Vscode: Select the file “lesson4/main.cwl”
- 1. Click on the “Terminal” menu
- 1. Click “Run Task…”
- 1. Select “Set Arvados project UUID”
+ 1. Click on `Additional info` in the upper right to expand the `info` panel
+ 1. Under `Project UUID` click the `Copy to clipboard` button
+1. Vscode: Select the file `lesson4/main.cwl`
+ 1. Click on the `Terminal` menu
+ 1. Click `Run Task…`
+ 1. Select `Set Arvados project UUID`
1. Paste the project UUID from workbench at the prompt
-1. Vscode: Select the file “lesson4/main.cwl”
- 1. Click on the “Terminal” menu
- 1. Click “Run Task…”
- 1. Select “Run CWL workflow on Arvados”
-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. Vscode: Select the file `lesson4/main.cwl`
+ 1. Click on the `Terminal` menu
+ 1. Click `Run Task…`
+ 1. Select `Run CWL workflow on Arvados`
+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. The results of this run will appear in the terminal when the run completes.
1. Workbench: Paste the workflow identifier into the search box
projects / arvados-vscode-cwl-training.git / blobdiff