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. 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: 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: 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: 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.
+ 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. 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. 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
projects / arvados-vscode-cwl-training.git / blobdiff