diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..defcde4 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +main.pdf filter=lfs diff=lfs merge=lfs -text diff --git a/.latexmkrc b/.latexmkrc index 7da747c..6c6740f 100644 --- a/.latexmkrc +++ b/.latexmkrc @@ -1,3 +1,9 @@ +sub createFolderStructure{ + system("bash ./folder-structure.sh"); +} + +createFolderStructure(); + $hash_calc_ignore_pattern{aux} = '^\\\\gdef\\\\minted@oldcachelist\{,' . '|^\s*default\.pygstyle,' diff --git a/folder-structure.sh b/folder-structure.sh new file mode 100644 index 0000000..a7b6dc5 --- /dev/null +++ b/folder-structure.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +find ./content -type d > folder_list.txt + +mkdir -p build +cd build +cat ../folder_list.txt | xargs mkdir -p +rm ../folder_list.txt \ No newline at end of file diff --git a/glossary.tex b/glossary.tex index e69de29..170d62b 100644 --- a/glossary.tex +++ b/glossary.tex @@ -0,0 +1 @@ +\newabbreviation{TAG}{TAGs}{Tandem Arrayed Genes} diff --git a/main.pdf b/main.pdf index b263fc2..01b837f 100644 Binary files a/main.pdf and b/main.pdf differ diff --git a/report.org b/report.org new file mode 100644 index 0000000..13817e9 --- /dev/null +++ b/report.org @@ -0,0 +1,44 @@ +#+title: Further development on FTAG Finder, a pipeline to identify Tandem Arrayed Genes +#+subtitle: Scientific project +#+author: Samuel Ortion +#+date: 2023-2024 +#+LATEX_CLASS: lamme2024 +#+LATEX_HEADER: \usepackage{sty/lamme2024} +#+bibliography: ../references.bib +#+exclude_tags: noexport + +# ref. https://write.as/dani/writing-a-phd-thesis-with-org-mode + +#+begin_export latex +\hypersetup{ + pdfauthor={Samuel Ortion}, + pdftitle={}, + pdfkeywords={duplicate genes, workflow management systems, pipeline}, + pdfsubject={}, + pdflang={English}} +{ +\pagenumbering{roman} +\hypersetup{hidelinks} +\tableofcontents +\printglossaries +} +#+end_export + +#+begin_center +duplicate genes, tandem arrayed genes, pipeline + +#+end_center + +* Context +** Duplicate genes +*** Duplication mechanism +*** Role in genome evolution +** Identification of duplicate genes +** FTAG Finder, a method to identify Families and Tandem Arrayed Genes +* Objectives + +* Tips :noexport: + +To export: +C-c C-e C-b l l + diff --git a/report.pdf b/report.pdf new file mode 100644 index 0000000..095f241 Binary files /dev/null and b/report.pdf differ diff --git a/report.tex b/report.tex new file mode 100644 index 0000000..0a01284 --- /dev/null +++ b/report.tex @@ -0,0 +1,23 @@ +% Created 2024-03-21 Thu 19:34 +% Intended LaTeX compiler: lualatex +\documentclass{scrreprt} + \usepackage{sty/lamme2024} +\author{Samuel Ortion} +\date{2023-2024} +\title{Further development on FTAG Finder, a pipeline to identify Tandem Arrayed Genes\\\medskip +\large Scientific project} +\hypersetup{ + pdfauthor={Samuel Ortion}, + pdftitle={Further development on FTAG Finder, a pipeline to identify Tandem Arrayed Genes}, + pdfkeywords={}, + pdfsubject={}, + pdfcreator={Emacs 29.2 (Org mode 9.7)}, + pdflang={English}} +\usepackage{biblatex} +\addbibresource{../references.bib} +\begin{document} + +\maketitle +\tableofcontents + +\end{document} diff --git a/sty/floatlefttextright.sty b/sty/floatlefttextright.sty index 0e44bfa..f031a06 100644 --- a/sty/floatlefttextright.sty +++ b/sty/floatlefttextright.sty @@ -1,31 +1,47 @@ % https://www.developpez.net/forums/d910711/autres-langages/autres-langages/latex/mise-forme/texte-recto-figures-verso/ % Solution by Martigan on Developpez.net +\iffalse \RequirePackage{afterpage} \RequirePackage{caption} \newcommand\@addfig{\relax} \newcommand\addfig[1]{\global\long\def\@addfig{#1}} \newcommand\@putfig{\@addfig\addfig{\relax}} -\newcommand\blankpage{% +\newcommand\flblankpage{% \null \vfill + \begin{figure}[H] \captionsetup{type=figure} % Warning: this could be faulty if tables are required \@putfig% + \end{figure} \vfill \thispagestyle{empty}% \clearpage% - \addtocounter{page}{-1} - \afterpage{\blankpage} + %\addtocounter{page}{-1} + \afterpage{\flblankpage} } + \iffalse % Example - \addfig{% + % Add this at the beggining of the document: + \afterpage{\flblankpage} + + \addfig{% \centering \includegraphics[scale=1]{Image1} \caption{Test} \label{Ima1} } \fi + +\fi + +\def\@floatplacement{\global\@topnum\c@topnumber + \global\@toproom \topfraction\@colht + \global\@botnum \c@bottomnumber + \global\@botroom \bottomfraction\@colht + \global\@colnum \ifodd\c@page\c@totalnumber\else\z@\fi%<<<<<<< + \@fpmin \floatpagefraction\@colht} diff --git a/sty/lamme2024.sty b/sty/lamme2024.sty index f383b87..cfce9d7 100644 --- a/sty/lamme2024.sty +++ b/sty/lamme2024.sty @@ -1,23 +1,10 @@ -\usepackage{graphicx} -\usepackage{tikz} -\usepackage{xcolor} -\usepackage{hyperref} - +% Font \usepackage{fontspec} \setmainfont{TeX Gyre Termes} % Times New Roman alternative \usepackage{setspace} \onehalfspacing % 1.5 interline spacing \defaultfontfeatures[\rmfamily,\sffamily]{Ligatures=TeX} -\addtokomafont{disposition}{\rmfamily} - -% Force text on right side, float on left side -\usepackage{sty/floatlefttextright} - -% Font -\RequirePackage{polyglossia} -\setmainlanguage{english} -%\setotherlanguage{french} % Float @@ -26,13 +13,13 @@ \RequirePackage{caption} \RequirePackage{subcaption} \RequirePackage{xcolor} - +\RequirePackage{csquotes} +\RequirePackage[english]{babel} % Math \RequirePackage{amsmath} \RequirePackage{amsthm} \RequirePackage{amssymb} - \usepackage{enumitem} \usepackage{lipsum} @@ -45,8 +32,8 @@ citestyle=authoryear-comp, natbib=true ]{biblatex} -\RequirePackage{doi} -\RequirePackage{xurl} +%\RequirePackage{doi} +%\RequirePackage{xurl} \RequirePackage{orcidlink} @@ -68,3 +55,13 @@ stylemods=longbooktabs, % do the adjustments for the longbooktabs styles, automake ]{glossaries-extra} + +\usepackage{hyperref} + +% Force text on right side, float on left side +% \usepackage{sty/floatlefttextright} + + +\makeglossaries +\makeindex +\renewcommand\maketitle{\include{titlepage}} diff --git a/sty/test_figurelefttextright.pdf b/sty/test_figurelefttextright.pdf new file mode 100644 index 0000000..02ca8c4 Binary files /dev/null and b/sty/test_figurelefttextright.pdf differ diff --git a/sty/test_figurelefttextright.tex b/sty/test_figurelefttextright.tex new file mode 100644 index 0000000..3e6dae8 --- /dev/null +++ b/sty/test_figurelefttextright.tex @@ -0,0 +1,19 @@ +\documentclass{book} + +\usepackage{floatlefttextright} +\usepackage{lipsum} +\usepackage{graphicx} + +\begin{document} + + \afterpage{\blankpage} +\lipsum{100} + + +\addfig{ + \includegraphics[width=\textwidth]{example-image-a} + \caption{Test figure} + \label{fig:Test figure} +} + +\end{document} diff --git a/titlepage.tex b/titlepage.tex index a3b18fe..2094dc5 100644 --- a/titlepage.tex +++ b/titlepage.tex @@ -11,13 +11,13 @@ \Large 2023--2024 - \hfill + \vfill - \Huge Samuel ORTION \orcidlink{0009-0001-0971-497X} + \Large Samuel ORTION \orcidlink{0009-0001-0971-497X} \vfill - \Huge + \LARGE Development of a Nextflow\footnote{We still need to decide which workflow manager to choose: Nextflow or Snakemake} pipeline for FTAG Finder, a duplicate gene detection tool, and improvement of the existing Galaxy implementation