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What about adding also conda environments to the mix #8
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Good point. Also thinking about vagrant. Could you elaborate on multi-platform? For me docker solves this very nicely, in the sense that it works on linux, windows and mac (the latter two need virtualbox but fine). I don't use conda envs enough for sharing environments but someone once told me that My favourite approach is to use conda inside docker. I have a shell script which does the equivalent of |
In general you can create conda environment that are platform specific if you depends on packages that are available only on one platform. Otherwise they should work across OS X, Windows and Linux. As a non completely trivial (but simple) example, I created a demo on mybinder using only a conda environment, and the environment was not created on linux: https://github.com/Photon-HDF5/Photon-HDF5-Converter I currently don't run virtual machines but work on Windows, OS X and Linux using only conda. A lightweight approach that works if you use mostly standard and homebuild packages. |
Found this slide (and the next 2 going down) on using snakemake with conda: http://slides.com/johanneskoester/snakemake-broad-2015#/23/3 |
-1 on specifically saying we'll support conda in the prototype; +1 on saying that we're open to including it. |
From talking to people it seems the pragmatists say: conda is nice but (often) isn't enough so you need something like docker (mainly related to lots of software not having conda packages but you can install them on a linux OS pretty easily). So I would vote for us saying "docker is the starting point, inside it you (the scientists) can do as you please" |
On Sat, Feb 27, 2016 at 2:36 PM, Tim Head [email protected] wrote:
I use conda environments on 3 platforms for python code+cython extensions If you depend on C/C++ libraries not included in Anaconda then yes, there I think docker is great but I fear that making it absolutely necessary will For the current proposal I don't think this detail is an issue but, in |
On Sun, Feb 28, 2016 at 1:40 AM Antonino Ingargiola <
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Absolutely - I still expect to see many people using their own paper |
+1 We need to start with something concrete, which is Docker containers. But we can add other options later. In fact, we have, if we want this to last for longer than the latest fad in computing technology. |
Docker containers are great, but oftentimes the software is simple enough that the environment can be reproduced with conda. This approach has also the benefit to be multi-platform.
It is a slightly more fragile approach but I think is good enough in many cases and a big improvement from manual installation.
In the spirit of "not changing you tools" it makes sense to add conda to the mix.
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