Switch to Anaconda for R and Git install

[biologyguy]

It seems that software installation instructions could be significantly streamlined by using Anaconda for R and git, with the added advantage of not requiring admin privileges.

$: conda install git
$: conda install -c r r-essentials

Are there reasons for separate installations that I'm not seeing?

[iglpdc]

Yes, but people using Windows will still need to install some sort of shell for the Unix lesson. By using Git Bash we kill to birds with a stone for them. Also note that we have workshops in MATLAB (and maybe other languages in the future), which may not conda-installable.

In any case, it could be a good thing to mention in the wiki.

[chendaniely]

This might be a tangent. but does the R kernel work for you in the jupyter notebook?
last time I tried to install r-essentials, I didn't see an R kernel for the notebooks.

Also, was just about to make the windows bash comment before Ivan beat me to it.

[biologyguy]

Ya, I've used R in Jupyter (on Mac), but it was... 6 months ago maybe? Haven't tried recently.

Edit: I just re-installed r-essentials and fired up Jupyter. All seems to be working.

As for Unix on Windows, have you guys ever used the Gnu on Windows toolkit? I've found it really easy to use when I needed to develop in Windows.
It would be a different install, vs the Git for Windows, but I think it could still be a net gain overall if conda could be used for everything else. I might try it with an upcoming workshop to see how it goes.
I do see the issue for Matlab-based workshops however...

[rgaiacs]

Yes, but people using Windows will still need to install some sort of shell for the Unix lesson.

Actually, conda will install bash for you. 😄 If you run bash on Conda prompt after install git you will get the Unix shell (Mingw-w64). Some configuration is broken and because of it you can't get Git when you start Bash from Conda prompt but it works if you open C:\Users\YourName\Anaconda3\Library\bin\bash.exe.

And you can create your first commit.

Notes:

1. Make isn't available on Conda. 😢
2. I didn't test R.

[chendaniely]

automake and cmake are on conda-forge. is that the same thing?

[rgaiacs]

@biologyguy @iglpdc @chendaniely Any progress on this one?

[biologyguy]

@rgaiacs This fell off my radar. Do you think it's worth following up with? I can just close out the comment if people are generally happy with Git for Windows.

[rgaiacs]

Do you think it's worth following up with? I can just close out the comment if people are generally happy with Git for Windows.

I always thought that Software Carpentry tried to use on the workshop the installation procedure with more market share because learners would find it some where else on the internet when searching another time. Based on that I would say that "we" are happy with Git for Windows. Unfortanatelly we aren't happy that Git for Windows doesn't include some tools like nano, make, man, ...

[biologyguy]

Well, the Gnu on Windows toolkit comes with some of the features you're after. It looks like we'll be setting up another workshop this spring, so I'll probably adapt our workshop fork to switch over to anaconda and GoW.

[biologyguy]

Merge with issue #395