X-Git-Url: https://git.arvados.org/arvados-vscode-cwl-training.git/blobdiff_plain/f07c87d740c5d60985311da49fec7e29e5104c79..21bdf14c7c725492cbdde9b3922fa90878c7df66:/README.md diff --git a/README.md b/README.md index 188ca26..89581a1 100644 --- a/README.md +++ b/README.md @@ -11,12 +11,22 @@ Code (abbreviated "vscode") to develop CWL workflows on Arvados. ## 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` @@ -24,29 +34,32 @@ 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. 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. 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` ![](images/Extensions.png) + 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` ![](images/RemoteExplorer.png) + 1. At the top of the Remote Explorer panel choose `SSH targets` ![](images/SSHTargets.png) + 1. Click `Add New` ![](images/AddNew.png) 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. 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` ![](images/Extensions.png) + 1. Search for "benten" and install `CWL (Rabix/Benten)` + 1. You should see a message `Extension is enabled on 'SSH: ...' and disabled locally.` +1. Vscode: On the left sidebar, choose `Explorer` ![](images/Explorer.png) + 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. Go to Arvados Workbench 1. Workbench: In the user menu, select `Current token` 1. Vscode: Click on the `Terminal` menu @@ -74,9 +87,13 @@ Code (abbreviated "vscode") to develop CWL workflows on Arvados. 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 @@ -86,14 +103,15 @@ Code (abbreviated "vscode") to develop CWL workflows on Arvados. 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.txt` + 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 @@ -154,3 +172,17 @@ The `message` parameter will be taken from the file `lesson4/main-input.yaml`. 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.