vsmalladi / wdl101

wdl101 in the cloud

1. Join the wdl101 classroom: https://classroom.github.com/a/TROwS5WY

2. After joining, it will create a new github repo as https://github.com/schatzlab-teaching/wdl101-USERNAME. You can then launch the Codespace by clicking on the <> Code button, and then "Create codespace on main". This will boot a free virtual machine for you to use with 2 cores, 4 GB of RAM and 32 GB of local disk running ubuntu linux.

3. Verify it is running with

$ miniwdl run_self_test

4. Once you confirm miniwdl is running, clone the learn-wdl repo:

$ git clone https://github.com/openwdl/learn-wdl.git

5. Try opening the WDL code in the Explorer such as learn-wdl/1_script_examples/1_hello_worlds/3_hello_input_task/input-task.wdl. It will ask you to install the WDL syntax highlighter. I recommend you do, as it will make it easier to read the code.

6. Try out the examples inside. For example:

$ cd learn-wdl/1_script_examples/1_hello_worlds/3_hello_input_task
$ miniwdl run input-task.wdl "WriteGreeting.name=Mike WDL Schatz"
...
$ cat _LAST/out/WriteGreeting.response/stdout.txt 
hello Mike WDL Schatz!

7. If you close the window, navigage to https://github.com/schatzlab-teaching and go to your private repo. From there you can relaunch your code environment. You can also navigate to https://github.com/codespaces to see your active codespaces.

8. Make sure to review the codespaces documentation, especially how to sync code inside the virtual machine back to the repo: https://docs.github.com/en/codespaces/getting-started/quickstart