.latexmkrc

@@ -2,7 +2,7 @@ sub createFolderStructure{
    system("bash ./folder-structure.sh");
 }
 
-# createFolderStructure();
+createFolderStructure();
 
 $hash_calc_ignore_pattern{aux} =
 '^\\\\gdef\\\\minted@oldcachelist\{,'

Makefile

@@ -16,6 +16,4 @@ bib:
 glossaries:
 	makeglossaries -d build $(SOURCE)
 
-index:
-	makeindex -d build $(SOURCE)
 .PHONY: build

figures/tag-definition.tex

@@ -5,9 +5,8 @@
 
 \usepackage{tikz}
 
+
 \begin{document}
-\definecolor{lammegreen}{HTML}{017d79}
-\definecolor{lammeblue}{HTML}{0050b4}
 \usetikzlibrary{positioning}
 \usetikzlibrary{decorations.pathreplacing}
 
@@ -22,28 +21,28 @@
   \draw[-,very thick] (-6,0) to (6,0);
   % Gene blocks
   \node[rectangle,fill=orange,minimum height=0.5cm, minimum width=1cm] (orange1) at (-5,0) {};
-  \node[rectangle,fill=lammegreen,minimum height=0.5cm, minimum width=1cm] (green1) [right=of orange1] {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green1) [right=of orange1] {};
   \node[rectangle,fill=red,minimum height=0.5cm, minimum width=1cm] (red1) [right=of green1] {};
-  \node[rectangle,fill=lammegreen,minimum height=0.5cm, minimum width=1cm] (green2) [right=of red1] {};
-  \node[rectangle,fill=lammegreen,minimum height=0.5cm, minimum width=1cm] (green3) [right=of green2] {};
-  \node[rectangle,fill=lammegreen,minimum height=0.5cm, minimum width=1cm] (green4) [right=of green3] {};
-  \node[rectangle,fill=lammeblue,minimum height=0.5cm, minimum width=1cm] (blue1) [right=of green4] {};
-  \node[rectangle,fill=lammeblue,minimum height=0.5cm, minimum width=1cm] (blue2) [right=of blue1] {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green2) [right=of red1] {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green3) [right=of green2] {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green4) [right=of green3] {};
+  \node[rectangle,fill=blue,minimum height=0.5cm, minimum width=1cm] (blue1) [right=of green4] {};
+  \node[rectangle,fill=blue,minimum height=0.5cm, minimum width=1cm] (blue2) [right=of blue1] {};
   \node[rectangle,fill=orange,minimum height=0.5cm, minimum width=1cm] (orange2) [right=of blue2] {};
 
   % Homology links
 
   \draw[-,orange, bend left=40] (orange1) to coordinate[dot] node[nod] {$\mathrm{TAG}_7$} (orange2);
 
-  \draw[-,lammegreen,bend right=40] (green1) to (green2)
+  \draw[-,green,bend right=40] (green1) to (green2)
   (green2) to (green3)
   (green3) to (green4);
-  \draw[-,lammegreen,bend left=40] (green1) to (green3)
+  \draw[-,green,bend left=40] (green1) to (green3)
   (green1) to coordinate[dot] node[nod] {$\mathrm{TAG}_3$}(green4);
-  \draw[-,lammegreen,bend right=40] (green1) to (green2)
+  \draw[-,green,bend right=40] (green1) to (green2)
   (green2) to (green4);
 
-  \draw[-,lammeblue, bend left=40] (blue1) to  coordinate[dot] node[nod] {$\mathrm{TAG}_0$} (blue2);
+  \draw[-,blue, bend left=40] (blue1) to  coordinate[dot] node[nod] {$\mathrm{TAG}_0$} (blue2);
 \end{tikzpicture}
 
 \end{document}

report.org

@@ -9,8 +9,13 @@
 #+exclude_tags: noexport
 #+options: H:7
 #+options: toc:nil
+#+MACRO: conditional-header (eval (concat "#+header: :results output " (print-to-string org-export-current-backend)))
+# ref. conditional-header https://emacs.stackexchange.com/a/64340/41374
+
+
 # ref. https://write.as/dani/writing-a-phd-thesis-with-org-mode
 
+
 #+name: acronyms
 | key        | abbreviation | full form                                  |
 |------------+--------------+--------------------------------------------|
@@ -48,12 +53,9 @@
 #+end_center
 
 #+begin_export latex
-{
-\hypersetup{linkcolor=black}
 \tableofcontents
 \listoffigures
 \listoftables
-}
 #+end_export
 
 [[printglossaries:]]
@@ -152,21 +154,19 @@ In this step, the typical tool involved is =BLAST= (Basic Local Alignment Search
 
 Several =BLAST= metrics can be used as an homology measure, such as bitscore, identity percentage, E-value or variations of these. The choice of metrics can affect the results of graph clustering in the following step, and we should therefore chose them carefully [cite:@gibbonsEvaluationBLASTbasedEdgeweighting2015].
 **** Identification of gene families
-Based on the homology links between each pair of genes, we construct an undirected weighted graph whose vertices correspond to genes and edges to homology links between them.
+Based on the homology links between each pair of genes, we construct a undirected weighted graph whose vertices correspond to genes and edges to homology links between them.
 We apply a graph clustering algorithm on the graph in order to infer the gene families corresponding to densely connected communities of vertices.
 
+FTAG Finder proposes three clustering algorithm alternatives: single linkage, Markov Clustering [cite:@vandongenNewClusterAlgorithm1998] or Walktrap [cite:@ponsComputingCommunitiesLarge2005].
+**** Detection of TAGs
+The final step of FTAG Finder consists in the identification of gls:TAG from the gene families and the positions of genes.
+For a given chromosome, the tool seeks genes belonging to the same family and located close to each other. The tool allows a maximal number of genes between the homologous genes, with a parameter set by the user. Ref:fig:tag-definitions is a schematic representation of some possible gls:TAG positioning on a genome associated with their definition in FTAG Finder /Find Tags/ step.
 #+begin_export latex
 \fladdfig{
 	\includegraphics[width=.9\linewidth]{./figures/tag-definition.pdf}
 	\caption[Schematic representation of TAG definitions]{\label{fig:tag-definitions} Schematic representation of TAG definitions. Several genes are represented on a linear chromosome. The red box represent a singleton gene. Orange boxes represent a TAG with two duplicate genes seperated by 7 other genes ($\mathrm{TAG}_7$). Four green boxes constitute a TAG, the gene at the extremities are seperated by three genes ($\mathrm{TAG}_3$. The two blue boxes represents a TAG with two genes next to each other $\mathrm{TAG}_0$. The bended edges represents the homology links between each pair of genes of a TAG.}}
 #+end_export
 
-
-FTAG Finder proposes three clustering algorithm alternatives: single linkage, Markov Clustering [cite:@vandongenNewClusterAlgorithm1998] or Walktrap [cite:@ponsComputingCommunitiesLarge2005].
-**** Detection of TAGs
-The final step of FTAG Finder consists in the identification of gls:TAG from the gene families and the positions of genes.
-For a given chromosome, the tool seeks genes belonging to the same family and located close to each other. The tool allows a maximal number of genes between the homologous genes, with a parameter set by the user. Cref:fig:tag-definitions is a schematic representation of some possible gls:TAG positioning on a genome associated with their definition in FTAG Finder /Find Tags/ step.
-
 * Objectives for the internship
 ** Scientific questions
 The underlying question of FTAG Finder is the study of the evolutionary fate of duplicate genes in Eukaryotes.
@@ -180,17 +180,14 @@ Another objective of my internship will be to port FTAG Finder on a workflow man
 We will have to make a choice for the tool we will use.
 The two main options being Snakemake and Nextflow. Snakemake is a python powered workflow manager based on rules /à la/ GNU Make [cite:@kosterSnakemakeScalableBioinformatics2012]. Nextflow is a groovy powered workflow manager, which rely on the data flows paradigm [cite:@ditommasoNextflowEnablesReproducible2017]. Both are widely used in the bioinformatics community, and their use have been on the rise since they came out in 2012 and 2013 respectively [cite:@djaffardjyDevelopingReusingBioinformatics2023].
 
-#+begin_export latex
-\flstop
+#+begin_export html
+<h3>Bibliography</h3>
 #+end_export
 
-* References
-:PROPERTIES:
-:UNNUMBERED: t
-:END:
+#+print_bibliography:
 
 #+begin_export latex
-\printbibliography[heading=none]
+\flstop
 #+end_export
 
 #+begin_export latex
@@ -198,8 +195,7 @@ The two main options being Snakemake and Nextflow. Snakemake is a python powered
 \clearpairofpagestyles
 #+end_export
 
-
-* Summary
+** Summary
 :PROPERTIES:
 :UNNUMBERED: t
 :END:
@@ -220,10 +216,6 @@ Principle: construct vertex communities based on where an agent would get stuck
 
 #  LocalWords:  speciation Subfunctionalization Neofunctionalization
 #  LocalWords:  Pseudogenization
-# Local Variables:
-# eval: (progn (org-babel-goto-named-src-block "startup") (org-babel-execute-src-block) (outline-hide-sublevels 1))
-# End:
-
 * Setup :noexport:
 
 #+name: startup
@@ -233,3 +225,7 @@ Principle: construct vertex communities based on where an agent would get stuck
 
 #+RESULTS: startup
 : Loaded ./setup.el
+
+#  Local Variables:
+#  eval: (progn (org-babel-goto-named-src-block "startup") (org-babel-execute-src-block) (outline-hide-sublevels 1))
+#  End:

setup.org

@@ -40,7 +40,7 @@ See: [[https://emacs.stackexchange.com/a/41456/41374]]
                 \\makeindex
                 \\makeglossaries          "
              ;("\\part{%s}" . "\\part*{%s}")
-             ("\\chapter{%s}" . "\\chapter*{%s}")
+             ("\\chapter{%s}" . "\\chapter{%s}")
              ("\\section{%s}" . "\\section*{%s}")
              ("\\subsection{%s}" . "\\subsection*{%s}")
              ("\\subsubsection{%s}" . "\\subsubsection*{%s}")

sty/lamme2024.sty

@@ -52,8 +52,6 @@
 	natbib=true
 ]{biblatex}
 
-\renewcommand\bibname{References}
-
 \RequirePackage{doi}
 \RequirePackage{xurl}
 \RequirePackage{orcidlink}
@@ -65,7 +63,7 @@
 ]{doclicense}
 
 \RequirePackage[
-	%nameinlink,
+	nameinlink,
 	noabbrev
 	]{cleveref}
 
@@ -85,8 +83,7 @@
   urlcolor=primaryLink,
   linkcolor=primaryLink,
   anchorcolor=primaryLink,
-  citecolor=primaryCite,
-  %linktoc=page
+  citecolor=primaryCite
 }
 \newcommand*{\glsplainhyperlink}[2]{%
     \begingroup%
@@ -103,14 +100,6 @@
 \renewcommand{\Gls}[1]{{\hypersetup{hidelinks}%
   \oldGls{#1}}}%
 
-\let\oldglspl=\glspl
-\renewcommand{\glspl}[1]{{\hypersetup{hidelinks}%
-    \oldglspl{#1}}}%}
-
-\let\oldGlspl=\Glspl
-\renewcommand{\Glspl}[1]{{\hypersetup{hidelinks}%
-    \oldGlspl{#1}}}%}
-
 
 %\renewcommand*{\glstextformat}[1]{\begingroup\hypersetup{hidelinks}#1\endgroup}
 %\renewcommand*{\glsdohyperlink}[2]{%