ga4gh / Get-Started-with-GA4GH-APIs

ISMB 2022 tutorial on FASP and Starter Kit
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Docker desktop link on sessions starterkit readme points to docker compose #34

Closed ianfore closed 2 years ago

ianfore commented 2 years ago

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.

yash-puligundla commented 2 years ago

Thanks Ian. They are fixed.

ianfore commented 2 years ago

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
yash-puligundla commented 2 years ago

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?

ianfore commented 2 years ago

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.

ianfore commented 2 years ago

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.

yash-puligundla commented 2 years ago

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.

yash-puligundla commented 2 years ago

removed setup.md to avoid duplication of instructions. Pointing to this document instead.