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nix-bioinfo-pkgs-sharcnet

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  • Overview

    This package contains a collection of Nix expressions created by SHARCNET staff for some software packages in the field of bioinformatics. You can use them to install the associated packages into your Nix environment.

    These directions assume you have loaded the Nix module (this enables your Nix environment and makes the various Nix commands available)

    module load nix

    Obtaining the latest expressions

    If you don't yet have a copy of ~/nix-bioinfo-pkgs-sharcnet, you will need to clone a copy (use your SHARCNET credentials)

    cd ~
    git clone https://git.sharcnet.ca/asobhani/nix-bioinfo-pkgs-sharcnet.git
    cd ~/nix-bioinfo-pkgs-sharcnet
    ./install.sh

    If you already have a copy, you can update to the latest version

    cd ~/nix-bioinfo-pkgs-sharcnet
    git pull
    ./install.sh

    Using an expression

    Once you have a copy of the expressions you can use nix-env to install, update, or remove them from your environment.

    Installing an expression

    To install (or update) a package pass the corresponding file (replace package.nix in what follows) to nix-env using the --file option

    nix-env --install --file package.nix

    You can also copy or symlink the file into your ~/.nix-defexpr directory and then refer to it as a top-level attribute (replace package with the base name of the copied file)

    nix-env --install --attr package

    Removing

    To remove a package you first need to figure out its name (generally, but not necessarily, the same as the name of the Nix expression file)

    nix-env --query

    Then you (replace package with the package name)

    nix-env --uninstall package

    Reverting

    To undo the last install/update/remove command

    nix-env --rollback