From e16913e3d7571320bdda508f5bcb7f288de522de Mon Sep 17 00:00:00 2001 From: Samuel Ortion Date: Thu, 21 Mar 2024 19:36:09 +0100 Subject: [PATCH] Migrating to org-mode --- .gitattributes | 1 + .latexmkrc | 6 +++++ folder-structure.sh | 8 ++++++ glossary.tex | 1 + main.pdf | Bin 55202 -> 130 bytes report.org | 44 +++++++++++++++++++++++++++++++ report.pdf | Bin 0 -> 68780 bytes report.tex | 23 ++++++++++++++++ sty/floatlefttextright.sty | 24 ++++++++++++++--- sty/lamme2024.sty | 33 +++++++++++------------ sty/test_figurelefttextright.pdf | Bin 0 -> 24048 bytes sty/test_figurelefttextright.tex | 19 +++++++++++++ titlepage.tex | 6 ++--- 13 files changed, 140 insertions(+), 25 deletions(-) create mode 100644 .gitattributes create mode 100644 folder-structure.sh create mode 100644 report.org create mode 100644 report.pdf create mode 100644 report.tex create mode 100644 sty/test_figurelefttextright.pdf create mode 100644 sty/test_figurelefttextright.tex 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\{,' . 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../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 0000000000000000000000000000000000000000..095f2410b95d724ea247fc2e7fb052b1a7679ed1 GIT binary patch literal 68780 zcmdSA1&k#|%rQx-?p%GXnHXtL=!Ppv>mlwz&Ze{Cg 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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 +% 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\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