Binder quick-start

[hehouts]

Hey, I made a binder!

And it wasnt as hard as I thought it would be! Maybe you want to make one too!

For context, this is the one I made: Lab 14 Binder. Its to teach a class on intro to command line for students that are pretty well versed in tidyverse, but only within R studio.

I followed this "Zero to Binder" tutorial (selected the R option), and it was fantastic.

Definitely there is some important thing to consider when your binder has large-ish files in it, and it has to do with making a PostBuild file. I didnt have that problem, so investigating how to do this is left as an exercise for the reader.

additionally, I yoinked some formatting from this cdfe binder set up: https://github.com/nih-cfde/training-rstudio-binder

Addtl useful tips from lab folks:

@ctb: "if you can get the conda environment right, that’s a critical step - and you can do it outside of a binder"
(I think I did that in mine, by making an .binder/environment.yml with the conda environment I wanted. I didnt really do anything to tell it to use conda, it just... worked!)

@jessicalumian:
"I’ve had problems with having a different version of python in my conda environment and on a terminal on JupyterLab.
When I need to create a new kernel for the jupyter environment this has worked for me:
Create virtual environment with mmh3 and sourmash and activate it.

# starting from (base) environment 
conda create -n mmh3_sourmash -c bioconda mmh3 sourmash
conda activate mmh3_sourmash
Install ipykernel, which can create kernel.json file needed by jupyter notebook to create a kernel with the virtual env software.
# inside (mm3_sourmash) environment
# used mamba because it solved issues that conda didn't
mamba install ipykernel
Register kernel spec
# inside (mm3_sourmash) environment
# ipython kernel install --user --name=new-env (I used the same name as conda virtual env for clarity)

ipython kernel install --user --name=mmh3_sourmash

Now the kernel mmh3_sourmash will be an kernel available to Jupyter."

[ctb]

this is fantastic, hannah - thanks!