1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
|
\documentclass[notoc]{tufte-book} % `notoc` suppresses TL custom TOC, reverts to standard LaTeX
\hyphenation{HMMER}
\input{titlepage} % definitions for \maketitle
\bibliographystyle{unsrtnat-brief} % customized natbib unsrtnat. Abbrev 3+ authors to ``et al.''
\begin{document}
\setcounter{tocdepth}{2} % 0=chapters 1=sections 2=subsections 3=subsubsections? 4=paragraphs
\input{inclusions/inclusions.def} % snippets captured from output, by gen-inclusions.py
\maketitle
\input{copyright}
\begin{adjustwidth}{}{-1in} % TL \textwidth is quite narrow. Expand it manually for TOC and man pages.
\tableofcontents
\end{adjustwidth}
\input{introduction}
\input{install}
\input{tutorial}
\input{pipeline}
\input{tabular}
\begin{adjustwidth}{}{-1in}
\chapter{Manual pages for HMMER programs}
\input{manpages}
\end{adjustwidth}
\begin{adjustwidth}{}{-1in}
\chapter{Manual pages for Easel miniapps}
\input{easel_manpages}
\end{adjustwidth}
\input{formats}
\input{ack}
\label{manualend}
% To create distributable/gitted 'distilled.bib' from lab's bibtex dbs:
% # uncomment the {master,lab,books}
% pdflatex main
% bibdistill main.aux > distilled.bib
% # restore the {distilled}
%
\nobibliography{distilled}
%\nobibliography{master,lab,books}
\end{document}
|
