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

diff --git a/README.md b/README.md
index e1cfd7b5a21062edad227ee98aa96f7d0193c8d5..c3a39c811ad343a59eece20893cbd155e395bd24 100644 (file)
--- a/README.md
+++ b/README.md
@@ -2,20 +2,31 @@ 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

 
 ## 1. SSH Setup
 
 1. (Windows only) Install git for windows [https://git-scm.com/download/win](https://git-scm.com/download/win)
 
 ## 1. SSH Setup
 
 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: Paste the key into `Public key` and enter something for `name`
    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`


@@ -23,17 +34,17 @@ Code (abbreviated "vscode") to develop CWL workflows on Arvados.
    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. 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 `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`
 
 ## 2. VSCode setup
 
 1. Install [Visual Studio Code](https://code.visualstudio.com/) and start it up
    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. 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. 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`


@@ -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
 

-# 3. 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