Commit 76710f3a authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros

Updated bibliography, added support for more figures.

parent 94973ea3
...@@ -15,6 +15,7 @@ LIBREOFFICE := libreoffice ...@@ -15,6 +15,7 @@ LIBREOFFICE := libreoffice
# Pictures. # Pictures.
DIA := dia DIA := dia
DOT := dot DOT := dot
FIG2DEV := fig2dev
CONVERT := convert CONVERT := convert
GNUPLOT := gnuplot GNUPLOT := gnuplot
FONTSIZE := 20 FONTSIZE := 20
...@@ -25,10 +26,10 @@ FONTSIZE := 20 ...@@ -25,10 +26,10 @@ FONTSIZE := 20
# Find the input files. # Find the input files.
SRC := $(basename $(shell grep -l '\\begin{document}' *.tex)) SRC := $(basename $(shell grep -l '\\begin{document}' *.tex))
DIA_PIC := $(basename $(shell ls *.dia)) DIA_PIC := $(basename $(shell ls *.dia))
FIG_PIC := $(basename $(shell ls *.fig))
GNP := $(basename $(shell ls *.gnp)) GNP := $(basename $(shell ls *.gnp))
PIC_EXT := dot gif jpg png ppm svg xcf PIC_EXT := dot gif jpg png ppm svg xcf bmp
PIC := $(foreach I, $(PIC_EXT), $(basename $(shell ls *.$I))) PIC := $(foreach I, $(PIC_EXT), $(basename $(shell ls *.$I)))
#PIC_EPS := $(addsuffix .eps, $(PIC))
# Output. # Output.
PDF := $(addsuffix .pdf, $(SRC)) PDF := $(addsuffix .pdf, $(SRC))
...@@ -43,10 +44,12 @@ TNP := $(addsuffix .tnp, $(GNP)) ...@@ -43,10 +44,12 @@ TNP := $(addsuffix .tnp, $(GNP))
# Semi-permanent files. # Semi-permanent files.
BIB := $(addsuffix .bbl, $(SRC)) BIB := $(addsuffix .bbl, $(SRC))
GLS := $(addsuffix .gls, $(GLS)) GLS := $(addsuffix .gls, $(GLS))
EPS := $(addsuffix .eps, $(DIA_PIC) $(GNP) $(PIC)) EPS := $(addsuffix .eps, $(DIA_PIC) $(FIG_PIC) $(GNP) $(PIC))
TEX_T_EXT := pstex pstex_t
TEX_T := $(foreach I, $(TEX_T_EXT), $(addsuffix .$I, $(FIG_PIC)))
# Do not delete the semi-permanent files automatically. # Do not delete the semi-permanent files automatically.
.PRECIOUS: $(BIB) $(GLS) $(EPS) .PRECIOUS: $(BIB) $(GLS) $(EPS) $(TEX_T)
# Disable built-in rules. # Disable built-in rules.
.SUFFIXES: .SUFFIXES:
...@@ -67,7 +70,7 @@ clean: ...@@ -67,7 +70,7 @@ clean:
rm -f $(foreach I, $(TMP), $(addsuffix .$I, $(SRC))) $(PNG) $(TNP) rm -f $(foreach I, $(TMP), $(addsuffix .$I, $(SRC))) $(PNG) $(TNP)
distclean: clean distclean: clean
rm -f $(PDF) $(RTF) $(DOC) $(BIB) $(EPS) rm -f $(PDF) $(RTF) $(DOC) $(BIB) $(EPS) $(TEX_T)
release: all clean release: all clean
...@@ -98,13 +101,25 @@ release: all clean ...@@ -98,13 +101,25 @@ release: all clean
%.eps: %.xcf %.eps: %.xcf
$(CONVERT) $< $@ $(CONVERT) $< $@
%.eps: %.bmp
$(CONVERT) $< $@
%.tnp: %.gnp $(DEP) %.tnp: %.gnp $(DEP)
echo "set terminal postscript color eps font \"default,$(FONTSIZE)\"" > $@ ;\ echo "set terminal postscript color eps font \"Helvetica,$(FONTSIZE)\"" > $@ ;\
cat $< >> $@ cat $< >> $@
%.eps: %.tnp %.eps: %.tnp
$(GNUPLOT) < $< > $@ $(GNUPLOT) < $< > $@
%.eps: %.fig
$(FIG2DEV) -L eps $< $@
%.pstex: %.fig
$(FIG2DEV) -L pstex $< $@
%.pstex_t: %.fig %.pstex
$(FIG2DEV) -L pstex_t -p $(word 2, $^) $< $@
# BibTeX targets (called recursively). # BibTeX targets (called recursively).
...@@ -130,7 +145,7 @@ release: all clean ...@@ -130,7 +145,7 @@ release: all clean
# LaTeX build targets. # LaTeX build targets.
%.aux: %.tex $(EPS) %.aux: %.tex $(EPS) $(TEX_T)
$(TEX) $< ;\ $(TEX) $< ;\
if (grep -s "LaTeX Warning: Citation" $*.log); then \ if (grep -s "LaTeX Warning: Citation" $*.log); then \
$(MAKE) $*.bbl ;\ $(MAKE) $*.bbl ;\
...@@ -142,6 +157,9 @@ release: all clean ...@@ -142,6 +157,9 @@ release: all clean
while (grep -s "Rerun to get cross-references right." $*.log); do \ while (grep -s "Rerun to get cross-references right." $*.log); do \
$(TEX) $< ;\ $(TEX) $< ;\
done ;\ done ;\
while (grep -s "Rerun to get /PageLabels entry." $*.log); do \
$(TEX) $< ;\
done ;\
while (grep -s "LaTeX Warning: There were undefined references" $*.log); do \ while (grep -s "LaTeX Warning: There were undefined references" $*.log); do \
$(TEX) $< ;\ $(TEX) $< ;\
done ;\ done ;\
......
@article{ KLIB, @article{ KLIB,
keywords = {jlaros_prep}, keywords = {jlaros, top},
author = "Anvar, S.Y. and Khachatryan, L. and Pulyakhina, I. and author = "Anvar, S.Y. and Khachatryan, L. and Vermaat, M. and van Galen, M.
van Galen, M. and Laros, J.F.J.", and Pulyakhina, I. and Ariyurek, Y. and Kraaijeveld, K. and den Dunnen, J.T.
title = "Applications of kmer profiling in omics data analysis.", and de Knijff, P. and 't Hoen, P.A.C. and Laros, J.F.J.",
journal = "In preparation", title = "Determining the quality and complexity of next-generation
year = 2013 sequencing data without a reference genome.",
journal = "Genome Biol.",
month = dec,
day = 17,
year = 2014,
volume = 15,
issue = 12
} }
@article{ TSSV, @article{ TSSV,
keywords = {jlaros_prep}, keywords = {jlaros, top},
author = "Anvar, S.Y. and van der Heijden, J.W.F. van der Gaag, K.J. and author = "Anvar, S.Y. and van der Gaag, K.J. and van der Heijden, J.W.F. and
Vossen, R.H.A.M. and Buermans, H.P.J. and Veltrop, M.H.A.M. and Veltrop, M.H.A.M. and Vossen, R.H.A.M. and de Leeuw, R.H. and Breukel, C. and
Verbeek, J.S. and den Dunnen, J.T. and de Knijff, P. and Laros, J.F.J.", Buermans, H.P.J. and Verbeek, J.S. and de Knijff, P. den Dunnen, J.T. and
title = "Targeted characterisation of short structural variation.", Laros, J.F.J.",
journal = "In preparation", title = "{TSSV}: a tool for characterization of complex allelic variants in
year = 2013 pure and mixed genomes.",
journal = "Bioinformatics",
month = jun,
day = 15,
volume = 30,
issue = 12,
year = 2014
} }
@article{ GONLPOS, @article{ GONLPOS,
...@@ -426,3 +438,209 @@ Number="6", ...@@ -426,3 +438,209 @@ Number="6",
Pages="1026--1032", Pages="1026--1032",
Month="Dec" Month="Dec"
} }
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keywords={jlaros},
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ISSN={1935-5548},
url={http://dx.doi.org/10.2337/dc14-0195},
DOI={10.2337/dc14-0195},
number={12},
journal={Diabetes Care},
publisher={American Diabetes Association},
author={Lips, M.A. and Van Klinken, J.B. and van Harmelen, V. and Dharuri, H.
K. and 't Hoen, P.A.C. and Laros, J.F.J. and van Ommen, G.-J. and Janssen,
I.M. and Van Ramshorst, B. and Van Wagensveld, B.A. and et al.},
year={2014},
month={Oct},
pages={3150–3156}
}
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title={Downregulation of the acetyl-CoA metabolic network in adipose tissue of
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DOI={10.1007/s00125-014-3347-0},
number={11},
journal={Diabetologia},
publisher={Springer Science + Business Media},
author={Dharuri, Harish and 't Hoen, Peter A.C. and van Klinken, Jan B. and
Henneman, Peter and Laros, Jeroen F. J. and Lips, Mirjam A. and el
Bouazzaoui, Fatiha and van Ommen, Gert-Jan B. and Janssen, Ignace and van
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year={2014},
month={Aug},
pages={2384–2392}
}
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title={Whole-genome sequence variation, population structure and demographic
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ISSN={1546-1718},
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publisher={Nature Publishing Group},
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url={http://dx.doi.org/10.1073/pnas.1312717110},
DOI={10.1073/pnas.1312717110},
number={14},
journal={Proceedings of the National Academy of Sciences},
publisher={Proceedings of the National Academy of Sciences},
author={Morikawa, H. and Ohkura, N. and Vandenbon, A. and Itoh, M. and
Nagao-Sato, S. and Kawaji, H. and Lassmann, T. and Carninci, P. and
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@article{Arner_2014,
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Tissue of Obese Subjects and in Obesity-Associated Cancer Cells},
volume={9},
ISSN={1932-6203},
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DOI={10.1371/journal.pone.0080274},
number={3},
journal={PLoS ONE},
publisher={Public Library of Science (PLoS)},
author={Arner, Erik and Forrest, Alistair R. R. and Ehrlund, Anna and Mejhert,
Niklas and Itoh, Masayoshi and Kawaji, Hideya and Lassmann, Timo and
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editor={Wu, QiongEditor},
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keywords={jlaros},
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volume={507},
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number={7493},
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publisher={Nature Publishing Group},
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pages={455–461}
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...@@ -2,6 +2,10 @@ ...@@ -2,6 +2,10 @@
\usepackage{graphicx} \usepackage{graphicx}
\usepackage[style=authortitle, sorting=ynt, dashed=false,
maxnames=99]{biblatex}
\addbibresource{../jfjlaros.bib}
\makeindex \makeindex
\begin{document} \begin{document}
...@@ -13,10 +17,11 @@ This is in the main file. ...@@ -13,10 +17,11 @@ This is in the main file.
\input{auxilary} \input{auxilary}
\section{Three} \section{Three}
Cite a paper~\cite{MMM}. %Cite a paper~\cite{MMM}.
\section{Four} \section{Four}
Refer back to Section~\ref{sec:one}. Refer back to Section~\ref{sec:one}.
\printbibliography[heading=none, keyword=jlaros]
\section{Five} \section{Five}
\includegraphics[width=\textwidth]{flow} \includegraphics[width=\textwidth]{flow}
...@@ -24,7 +29,7 @@ Refer back to Section~\ref{sec:one}. ...@@ -24,7 +29,7 @@ Refer back to Section~\ref{sec:one}.
\includegraphics[width=\textwidth]{plot} \includegraphics[width=\textwidth]{plot}
\bibliography{../bioinf,../jfjlaros}{} %\bibliography{../bioinf,../jfjlaros}{}
\bibliographystyle{plain} %\bibliographystyle{nar}
\end{document} \end{document}
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