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