GNU guix with conda

When we have GNU Guix we have no longer a need for bootstrapping conda. GNU Guix replaces miniconda!

Get a rock-solid conda bootstrap from GNU Guix. At this point conda gets build in a reproducible way using the latest packages. To make the conda build system even more reproducible we'll need to propagate gcc etc.

It already works great!

This repository is a temporary "channel" of sorts for conda and its dependencies, to be used before these packages make their way to mainline guix.

Install conda on GNU Guix

Checkout the repository and run

env GUIX_PACKAGE_PATH=guix-conda/ guix package -i conda

Now conda is in Guix. Run it after pasting the results of

guix package --search-paths

in your shell. Next

conda

    usage: .conda-real [-h] [-V] command ...

    conda is a tool for managing and deploying applications, environments and packages.

Finally, you'll need to create a clone because GNU Guix is read-only, so after this error

conda install bwa
CondaIOError: IO error: Missing write permissions in: /gnu/store/alk9r3rir93pjmv8im20f8xrvv90219z-python-3.5.2

set the name space to (for example) my_conda

conda create -n my_conda --clone=/gnu/store/alk9r3rir93pjmv8im20f8xrvv90219z-python-3.5.2

and use it from then on

conda install -n my_conda bwa

run the tool

~/.conda/envs/my_conda/bin/bwa

Install conda library

conda also installs as a library:

env GUIX_PACKAGE_PATH=../guix-conda/ guix package -i python python-conda

env PYTHONPATH=/home/wrk/.guix-profile/lib/python3.5/site-packages python3.5
Python 3.5.2
[GCC 4.9.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import conda
>>>