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KrishnaswamyLab / MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
GNU General Public License v2.0
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request: port to bioconda #73

Closed mheskett closed 6 years ago

mheskett commented 6 years ago

conda is an excellent package manager for python3 and seems like is gaining in popularity. Could you create a conda recipe for magic?

cimbusch commented 6 years ago

I totally would appreciate that as well. I do not have root access to execute the global installation command such as "sudo -H pip3 install .", it should be somehow possible to install it into user space. Usually I use bioconda for that.

The R installation worked but aborted with the error "Error: $ operator is invalid for atomic vectors"

pkathail commented 6 years ago

Will look into adding this -- thanks for the suggestion!

mg1655 commented 6 years ago

@cimbusch, there are a few ways to install locally with pip3, e.g.

pip3 install --user $USER . pip3 install --install-option='--prefix=$HOME' .

(replace $USER and $HOME to change install location)

scottgigante commented 6 years ago

MAGIC has been added to PyPi as magic-impute - I don't think we have any short term plans of adding to conda since Anaconda's native pip support is pretty good, so I'm closing this for now. Anyone who is interested is welcome to create a recipe to add to bioconda or conda-forge if they like.