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adokter / bioRad

R package for analysis and visualisation of biological signals in weather radar data
http://adokter.github.io/bioRad
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Test docker installation instructions on Windows #139

Closed peterdesmet closed 5 years ago

peterdesmet commented 6 years ago

https://github.com/adokter/bioRad/issues/137#issuecomment-423293284 got me thinking what functions require docker. The README currently states:

You only need to install Docker if:

  • you want to run the vol2bird algorithm.
  • you want to analyze NEXRAD data. The tools to convert NEXRAD data into ODIM format require Docker.

Is it for NEXRAD data only? Do you need it when reading an ODIM pvol file? I think it would be good to rephrase this a bit. And list the functions/function sections that require docker. Is it restricted to the functions from "Reading radar data" and "Creating vertical profiles of biological targets"?

adokter commented 6 years ago

Is it for NEXRAD data only?

No, also when running calculate_vp on an ODIM pvol file

Do you need it when reading an ODIM pvol file?

Not when reading the data into R (e.g. when making plots with plot.scan or project_as_ppi/plot.ppi), but you do when calculating a vertical profile with calculate_vp

list the functions/function sections that require docker.

Is it restricted to the functions from "Reading radar data" and "Creating vertical profiles of biological targets"?

yes

peterdesmet commented 6 years ago

Thanks, will clarify this in README when addressing #138

peterdesmet commented 6 years ago

The current installation instructions in the README say:

Docker needs local drives to be available for Docker containers. To enable:

  • right click the Docker (whale) icon on your task or menu bar
  • select settings -> shared drives
  • select the drives where you will be processing radar files
  • click apply

I didn't need to do this for Mac (and the instructions were thus a bit confusing): once installed I could use it right away by opening the app. Can someone test if the following installation instructions are good enough for Windows:

  1. Go to Docker Desktop.
  2. Download Docker for Windows or Mac (free login required) and follow the installation instructions.
  3. Open the Docker application. The Docker (whale) icon will appear in your menu bar and indicate if it is running correctly.
  4. In R do check_docker().
  5. You can now use the bioRad functionality that requires Docker.
peterdesmet commented 5 years ago

Docker requirements have been clarified in the README. But it would be good if someone can test the 5 steps of the "Installing Docker" on a Windows computer. @damianooldoni? Meanwhile, will bump this to milestone 0.5.0 as this is not blocking the release.

damianooldoni commented 5 years ago

Installing Docket Desktop only possible for machines running Windows 10. I have Windows 7 Professional on my laptop. From Docker website:

Requires Microsoft Windows 10 Professional or Enterprise 64-bit. For previous versions get Docker Toolbox.

You can find Docker Toolbox here: https://docs.docker.com/toolbox/overview/.

However, I get this error and I am not the only one: https://forums.docker.com/t/docker-quickstart-terminal-error-looking-for-vboxmanage-exe/35028.

adokter commented 5 years ago

Hi @damianooldoni @peterdesmet, earlier install instructions mentioned explicitly that only Microsoft Windows 10 Professional or Enterprise 64-bit will work, and Docker toolbox not, but I see that in rewriting documentation that has been removed. I will add it back.

So testing for Windows needs to be done on a Windows 10 Professional or Enterprise machine...

peterdesmet commented 5 years ago

Thanks for testing @damianooldoni. @adokter can you close this issue once done?

peterdesmet commented 5 years ago

@CeciliaNilsson709 @adokter could you test this one too on your Windows computer? Alternative is me doing it next week.

CeciliaNilsson709 commented 5 years ago

Reinstalled it just before to check the other issue, and those instructions work 👍. The only extra step I had was I had to "Share" my drive with Docker before I use calculate_vp, but that was straight forward.

adokter commented 5 years ago

The only extra step I had was I had to "Share" my drive with Docker

Those setup steps were described in an earlier version of the install instructions:

https://github.com/adokter/bioRad/blame/8a6a854be185925c3acf7871b31b561f7ab082ce/README.md#L66-L74

If these are still correct (@CeciliaNilsson709 ?), I would suggest keeping them

CeciliaNilsson709 commented 5 years ago

Docker gave a prompt where I could do it directly when I tried to run the command, but those instructions work too. So maybe good to include them just incase someone gets stuck on that for some reason?

adokter commented 5 years ago

It also seems the steps are a little different on Mac and Windows, so instructions get a bit lengthy:

Docker needs local drives to be available for Docker containers. To enable:

On Windows:

On Mac:

peterdesmet commented 5 years ago

Thanks!! See https://github.com/adokter/bioRad/pull/179 for an attempt to combine all information while keeping it succinct.

adokter commented 5 years ago

Thanks looking good, I'll merge the PR and close the issue 👍