Closed ianfore closed 2 years ago
Thanks Ian. They are fixed.
Thanks Yash.
Worked through everything on a Windows machine that had not even previously had python on it. Stepped through the set up. I installed Python 3.10.5 from the link in the setup readme Docker desktop was a bit tricky - it didn't run right first time. I had to run an update of WSL which Docker depends on.
I also set up a venv to run things from
>mkdir venvs
>python -m venv venvs/ismbtest
>.\venvs\ismbtest\Scripts\activate
>cd ismb-2022-ga4gh-tutorial\sessions\StarterKits\Part_1_DRS_WES
>pip install requests
>python scripts\populate-drs.py
This is wonderful. Thank you, Ian. I will add virtual env to the list.
Docker desktop was a bit tricky - it didn't run right first time. I had to run an update of WSL which Docker depends on.
Did you happen to capture the error/behavior when you tried to install docker desktop?
Did you happen to capture the error/behavior when you tried to install docker desktop?
'fraid not. :-) The install itself went OK. When I ran Docker Desktop it gave me an error and a link to go to update WSL.
I also ran through installing things for sessions/2 on top of what was set up for the Starter Kit sessions. It ran OK. Details as follows.
(ismbtest) C:\Users\<user>\fasp-scripts>pip install jupyter
(ismbtest) C:\Users\<user>\fasp-scripts>pip install .
(ismbtest) C:\Users\<user>\fasp-scripts>cd ..\ismb-2022-ga4gh-tutorial\sessions\2
(ismbtest) C:\Users\<user>\fasp-scripts> jupyter notebook
Thanks for your logs in issue #31 . I haven't tried to debug that yet. Can someone else try session 2 to see if they get the same problem? We may have to come back to your machine to sort the specific issues, but it would be good to get a sense whether it is a universal problem or not by trying it one someone else's machine.
When I ran Docker Desktop it gave me an error and a link to go to update WSL.
Good to know. As long as the error is not cryptic, we should be fine.
Thanks for your logs in issue https://github.com/ga4gh/ismb-2022-ga4gh-tutorial/issues/31 . I haven't tried to debug that yet. Can someone else try session 2 to see if they get the same problem? We may have to come back to your machine to sort the specific issues, but it would be good to get a sense whether it is a universal problem or not by trying it one someone else's machine.
Glad to hear it works fine on your machine. I didn't get a chance to debug either. But, hope that it's specific to my machine.
I have added create & activate venv steps to SETUP.md. We can add the specific pip install commands at the start of each of our tutorials.
removed setup.md to avoid duplication of instructions. Pointing to this document instead.
It should point to https://www.docker.com/products/docker-desktop/
Also note that installing docker desktop installs docker compose. See second section here https://docs.docker.com/get-started/08_using_compose/ So the second line to install Docker compose is not be necessary.