compare containers to VMs

coderefinery / reproducible-research

Reproducible research - Preparing code to be usable by you and others in the future

https://coderefinery.github.io/reproducible-research/

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compare containers to VMs #47

Closed wikfeldt closed 5 years ago

wikfeldt commented 5 years ago

since the differences are important

Sabryr commented 5 years ago

would it be too much if we have "virtual environments" in this comparison as well. My personal favourite to overcome hard compiled binaries is conda, not containers.

annefou commented 5 years ago

I definitely agree with you @Sabryr . I just discussed last week about developing a short tutorial on how to add new packages in conda.

wikfeldt commented 5 years ago

good point, i'll generalize the Containers episode to cover also conda and perhaps pipenv.

bast commented 5 years ago

Yay for pipenv :-)

annefou commented 5 years ago

is pipenv for python only or is it like conda (language agnostic)?

Sabryr commented 5 years ago

pipenv is only for python packages (it could contain compiled C) for example things you install with pip install. Conda is actually package manager in a sense. On Abel (out HPC cluster) I have several kernel dependent packages in conda with all binaries and GLIBC.

wikfeldt commented 5 years ago

good reference for the git+snakemake+conda+docker reproducible combo is this NBIS course: https://nbis-reproducible-research.readthedocs.io/en/latest/