An example of a LaTeX/knitr report setup containing a git commit revision number

Makefile

.PHONY: clean

PRJDIR := /path/to/project
DOCS := $(PRJDIR)/docs
RLIBS := /gscmnt/gc2801/analytics/idas/jira/BIO-1465/rpkgs
REPORTDIR := $(DOCS)/writeups
PDFLATEX := /home/archive/texlive-2015/2015/bin/x86_64-linux/pdflatex

writeup: $(REPORTDIR)/report.pdf

$(REPORTDIR)/%.pdf: $(REPORTDIR)/revision.tex $(REPORTDIR)/%.tex
    cd $(REPORTDIR) && $(PDFLATEX) $(REPORTDIR)/$*.tex
    cd $(REPORTDIR) && $(PDFLATEX) $(REPORTDIR)/$*.tex

$(REPORTDIR)/%.tex: $(REPORTDIR)/%.Rtex
    cd $(REPORTDIR) && R_LIBS=$(RLIBS) $(BIO_1597)/bin/knit-latex.r $<

$(REPORTDIR)/revision.tex:
    echo "% Autogenerated, do not edit" > $(REPORTDIR)/revision.tex
    echo "\\\\newcommand{\\\\revisiondate}{`git log -1 --format=\"%ad\" --date=short`}" >> $(REPORTDIR)/revision.tex
    echo "\\\\newcommand{\\\\revision}{`git log -1 --format=\"%h\"`}" >> $(REPORTDIR)/revision.tex

clean:
    bash -c "rm -fv $(REPORTDIR)/report.{aux,log,out,fff,ttt,tex,pdf}"
    rm $(REPORTDIR)/revision.tex

report.Rtex

\documentclass[10pt, letterpaper]{article}

% P R E A M B L E %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{parskip}                                    % no-indentation with a space between paragraphs
\usepackage{booktabs}                                   % for the tables
\usepackage[linkbordercolor={1 0 0}]{hyperref}          % for url labels
\usepackage{xcolor}                                     % for colors
\usepackage{fancyhdr}                                   % for customized headers
%\usepackage{float}                                     % for forcing figure placements in text
%\usepackage[nolists, nomarkers, tablesfirst]{endfloat}  % for place all figures at the end of the document
\usepackage{tikz}

\usetikzlibrary{
     positioning,                % for the relative node positioning
     shapes.multipart,           % for the rectangle split
     decorations.pathreplacing,  % for the brace comments
     calc                        % for the let command
}

\definecolor{pastelRed}{RGB}{251,180,174}
\definecolor{pastelBlue}{RGB}{179,205,227}
\definecolor{pastelGreen}{RGB}{204,235,197}
\definecolor{pastelPurple}{RGB}{222,203,228}
\definecolor{pastelYellow}{RGB}{254,217,166}

% setup an alternative font
\usepackage[T1]{fontenc}
\usepackage[sfdefault]{FiraSans}

% setup link colors
\hypersetup{
    colorlinks,
    linkcolor={red!80!black},
    citecolor={blue!50!black},
    urlcolor={blue!60!black}
}

% include git revision info
\input{revision}

% header/footer style on the front page
\fancypagestyle{titlepage}{%
    \fancyhf{} % clear all header and footer fields
    \fancyfoot[C]{\bfseries \thepage} % except the center
    \fancyfoot[R]{\scriptsize{revision: \revision}} % except the right
    \renewcommand{\headrulewidth}{0pt}
    \renewcommand{\footrulewidth}{0pt}
}

% setup document headers and footers (for body pages)
\pagestyle{fancy}
\lhead{}
\chead{}
\rhead{\thepage}
\lfoot{}
\cfoot{}
%\rfoot{\scriptsize{\revisiondate \quad (\revision)}}
\rfoot{\scriptsize{revision: \revision}}

% C O M M A N D S %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\renewcommand{\abstractname}{Goal}
%% for inline R code: if the inline code is not correctly parsed, you will see a message
\newcommand{\rinline}[1]{SOMETHING WRONG WITH knitr}

% H E A D E R %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\title{Example Report}
\author{}
\date{\today}

% K N I T R  S E T U P %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% begin.rcode setup, include=FALSE
% opts_chunk$set(fig.path='figure/latex-', cache.path='cache/latex-')
%% end.rcode

% D O C U M E N T %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
\maketitle
\thispagestyle{titlepage}

\begin{abstract}
Blah. Blah.
\end{abstract}

\section{Overview}

The good stuff goes here.

\begin{figure}[h]
    \begin{center}
    \begin{tikzpicture}[scale=0.5]
        % ----- Reference Set -----
        % main chromosome line
        \draw [thick] (0,5) -- (10,5);

        % exon ``boxes''
        \path [fill=pastelRed!60] (1,4.5) rectangle (3, 5.5);
        \path [fill=pastelRed!70] (5,4.5) rectangle (7, 5.5);
        \path [fill=pastelRed!90] (8,4.5) rectangle (9.5, 5.5);

        % labels
        \node at (2,5) {1};
        \node at (6,5) {2};
        \node at (8.75,5) {3};
        \node [right] at (11,5) {Gene Blah};

        % ----- Target Set (Nimblegen) -----
        % main chromosome line
        \draw [thick] (0,3) -- (10,3);

        % exon ``boxes''
        \path [fill=pastelRed!60] (1,2.5) rectangle (3, 3.5);
        \path [fill=pastelRed!70] (5,2.5) rectangle (7, 3.5);
        \path [fill=pastelRed!90] (8,2.5) rectangle (9.5, 3.5);

        % labels
        \node at (2,3) {1};
        \node at (6,3) {2};
        \node at (8.75,3) {3};
        \node [right] at (11,3) {Gene Blah (Nimblegen Targets)};

        % ----- Target Set (IDT) -----
        % main chromosome line
        \draw [thick] (0,1) -- (10,1);

        % exon ``boxes''
        \path [fill=pastelRed!60] (1,0.5) rectangle (3, 1.5);
                \path [fill=pastelRed!90] (8,0.5) rectangle (9.5, 1.5);

        % labels
        \node at (2,1) {1};
        \node at (8.75,1) {3};
        \node [right] at (11,1) {Gene Blah (Target)};
    \end{tikzpicture}
    \end{center}
    \caption{An Example of Incomplete Chromosome Coverage}
    \label{fig:ChromFig}
\end{figure}

\end{document}