Shell – How to setup a separate bash environment with only GNU utilities on OS X

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For the last 5 years, I have used linux as my everyday OS for performing scientific computing. My work recently gave me a Mac that I will be the primary user for the next few months. I keep running into conflicts between the Free-BSD bash environment on the Mac and the GNU environment I am used to, both with bash scripts I have setup and as I try to run bash commands (coreutils, findutils, etc). I do not want to switch completely to the Free-BSD utilies as all my other computers as well as our HPC's use linux with the GNU utilities. I want to avoid having to maintain two sets of bash scripts and also having to remember the nuances of the differing flags and functionalities between the two systems. I also do not want to break any of Mac's gui utilites etc that other users will use (either in the next few months or when it is given to someone else). Additionally, responses to this related question warn against completely replacing the Mac Free-BSD utilities with GNU ones.

Is it possible to install/setup a separate bash environment to use only the GNU utilities while leaving the system Free-BSD ones in place? My expect the most promising option is setting up my $PATH variable to point to a directory containing the GNU executables (with their standard names) while ignoring the Free-BSD ones. How could I apply this to my cross-platform bash scripts? Are there alternative options worth considering?

Best Answer

First, this is about a lot more than just coreutils. The BSD equivalent to GNU findutils is also quite different, pretty much every command related to dynamic linkage is different, etc.

And then on top of that, you have to deal with versioning differences: OS X still ships a lot of older software to remain on GPL2 instead of GPL3, such as Bash 3.x instead of Bash 4.x. The autotools are also often outdated with respect to bleeding-edge Linux distros.

The answer to the core part of your question is, "Sure, why not?" You can use Homebrew to install all of these alternative GNU tools, then put $(brew --prefix coreutils)/libexec/gnubin and /usr/local/bin first in your PATH to make sure they're found first:

export PATH="$(brew --prefix coreutils)/libexec/gnubin:/usr/local/bin:$PATH"

If for some reason brew installs a package to another location, also include that in the PATH variable.

If you would rather only replace a few packages, the tricky bit is dealing with all the name changes. Whenever brew installs a program that already has an implementation in the core OS, such as when installing GNU coreutils, it names its version differently so that you can run either, depending on your need at the time. Instead of renaming all of these symlinks¹, I recommend that you fix all of this up with a layer of indirection:

$ mkdir ~/linux
$ cd ~/linux
$ ln -s /usr/local/bin/gmv mv
...etc for all the other tools you want to rename to cover OS versions
$ export PATH=$HOME/linux:$PATH
...try it out...

Once you're happy with your new environment, you can put export PATH=$HOME/linux:$PATH into your ~/.bash_profile.

That takes care of interactive use, either with bulk replacement or single application replacement.

Unfortunately, it does not completely solve the shell script problem, because sometimes shell scripts get their own environment, such as when launched from cron. In that case, you could modify the PATH at the top of each cross-platform shell script:

#!/bin/bash
export PATH="$HOME/linux:$(brew --prefix coreutils)/libexec/gnubin:/usr/local/bin:$PATH"

You do not need to make it conditional, since it is just offering the shell another place to look for programs.

Footnotes

  1. e.g. /usr/local/bin/gmv → ../Cellar/coreutils/$version/bin/gmv

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