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[arvados-vscode-cwl-training.git] / README.md

diff --git a/README.md b/README.md
index 3c66c19e4434aeda5bf07c97db189be607f6bca9..c3a39c811ad343a59eece20893cbd155e395bd24 100644 (file)
--- a/README.md
+++ b/README.md
@@ -2,43 +2,54 @@ These lessons give step by step instructions for using Visual Studio
 Code (abbreviated "vscode") to develop CWL workflows on Arvados.
 
 1. Set up SSH
 Code (abbreviated "vscode") to develop CWL workflows on Arvados.
 
 1. Set up SSH

-1. Install vscode and necessary 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
+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

 
 

-## SSH Setup
+## 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. Open bash shell (installed with git for Windows)
+   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. Shell: Run `ssh-keygen`

-   1. Shell: Look for `Your public key has been saved in /c/Users/MyUsername/.ssh/id_rsa.pub`
+      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: Run `cat /c/Users/MyUsername/.ssh/id_rsa.pub`

-   1. Shell: Highlight and copy the lines starting with `ssh-rsa …`
-1. Open Arvados workbench
+   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: 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: Paste the key into `Public key` and enter something for `name`

    1. Workbench: Go to `Virtual Machines` in the user menu
    1. Workbench: Go to `Virtual Machines` in the user menu

-   1. Workbench: Highlight and copy the value in in the "Command line" column.
+   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. 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 “do you want to continue connecting`
-   1. Shell: You should now be logged into the Arvados shell node.  Note:
-      it can take up to two minutes for the SSH key to be copied to
-      the shell node.  If it doesn't work the first time, wait 60
+   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.
       seconds and try again.

+   1. Shell: You should now be logged into the Arvados shell node.

    1. Shell: Log out by typing `exit`
 
    1. Shell: Log out by typing `exit`
 

-## VSCode setup
+## 2. VSCode setup

 
 1. Install [Visual Studio Code](https://code.visualstudio.com/) and start it up
 
 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: go to `Extensions` ![](images/Extensions.png)
+   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 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 for SSH Setup step 4.1
+   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. 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)`


@@ -56,7 +67,7 @@ Code (abbreviated "vscode") to develop CWL workflows on Arvados.
    1. Workbench: Copy the string following `ARVADOS_API_TOKEN=`
    1. Vscode: Paste the string at the `Value for ARVADOS_API_TOKEN` 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
+## 3. Register & run a workflow

 
 1. Vscode: Click on the `lesson1/main.cwl` file
    1. Click on the `Terminal` menu
 
 1. Vscode: Click on the `lesson1/main.cwl` file
    1. Click on the `Terminal` menu


@@ -69,7 +80,7 @@ Code (abbreviated "vscode") to develop CWL workflows on Arvados.
    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. 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. 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 `Run process`
    1. This should take you to a panel showing the workflow run status
 1. Workbench: workflow run status panel


@@ -78,31 +89,31 @@ Code (abbreviated "vscode") to develop CWL workflows on Arvados.
    1. Under `event type` choose `stdout`
    1. You should see your message
 
    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. Go to your desktop
 
 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. 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. Workbench: Go to `+NEW` and select `New project`

-   1. Enter a name for the project like `Lesson 2`
+   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. 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. 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. 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. Enter a name for this run like "Second training run"

    1. Click on `#main/message`
    1. A selection dialog box will appear
    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. 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. Click `Run process`
    1. This should take you to a panel showing the workflow run status
 1. Workbench: workflow run status panel


@@ -113,27 +124,27 @@ Code (abbreviated "vscode") to develop CWL workflows on Arvados.
    1. Click on `Download`
    1. Open the downloaded file.  It should have your results.
 
    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
 
 1. Workbench: Go to `+NEW` and select `New project`
 
 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. 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. 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. 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
 
    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.
 
 1. Workbench: Go to `+NEW` and select `New project`
 
 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. 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. 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