Don’t know what brew is? Checkout homebrew and install it.

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brew tap homebrew/science

Looks like homebrew/science is under very active development; there are currnetly 122 formulae and 50 open issues (44 open pull requests). Some notable tools: abyss, bedtools, bowtie, bwa, octave, samtools, tabix, tophat, and velvet.

To diff two non-versioned files add the --no-index option, i.e. git diff --color-words --no-index.

On occasion I have wanted to edit the original commit of my Git repo. If it were any other commit I would just do an interactive rebase to modify it but that isn’t possible with the original commit. However, you can do the rebase manually if you follow the process below:

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OLD_ROOT=$(git log --reverse --format=%h | head -n 1)
git checkout $OLD_ROOT

# If you want to add or remove files do so now and stage them using
# `git add` or `git rm`.

git commit --amend
NEW_ROOT=$(git rev-parse --short HEAD)

# This assumes you were on a branch when you started.
git checkout @{-1}

git rebase --onto $NEW_ROOT $OLD_ROOT

Based on: Can I remove the initial commit from a Git repo?