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Makefile
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R_OPTS=--no-save --no-restore --no-init-file --no-site-file # --vanilla, but without --no-environ
all: docs/1_geneticmaps.pdf \
docs/2_introqtl.pdf \
docs/3_multiqtl.pdf \
docs/4_mpp.pdf \
docs/5a_clearcode.pdf \
docs/5a_clearcode_withnotes.pdf \
docs/5b_rpack.pdf \
docs/5b_rpack_withnotes.pdf
docs/1_geneticmaps.pdf: 1_maps/1_geneticmaps.dvi 1_maps/1_geneticmaps.R
cd 1_maps;dvipdf 1_geneticmaps.dvi 1_geneticmaps.pdf
mv 1_maps/1_geneticmaps.pdf $@
1_maps/1_geneticmaps.dvi: 1_maps/1_geneticmaps.tex
cd 1_maps;latex 1_geneticmaps
cd 1_maps;latex 1_geneticmaps
cd 1_maps;latex 1_geneticmaps
1_maps/1_geneticmaps.tex: 1_maps/1_geneticmaps.Rnw 1_maps/clean_sweave.pl
cd 1_maps;echo "library(tools); Sweave(\"1_geneticmaps.Rnw\", pdf=FALSE)" | R --no-save --no-restore --quiet
cd 1_maps; clean_sweave.pl 1_geneticmaps
1-maps/1_geneticmaps.R: 1_maps/1_geneticmaps.Rnw
echo "library(tools); Stangle(\"1_geneticmaps.Rnw\")" | cd 1_maps;R --no-save --no-restore --quiet
docs/2_introqtl.pdf: 2_introqtl/2_introqtl.tex
cd 2_introqtl;pdflatex $(<F)
mv 2_introqtl/2_introqtl.pdf $@
docs/3_multiqtl.pdf: 3_multiqtl/3_multiqtl.tex
cd 3_multiqtl;pdflatex $(<F)
mv 3_multiqtl/3_multiqtl.pdf $@
docs/4_mpp.pdf: 4_mpp/4_mpp.tex
cd 4_mpp;pdflatex $(<F)
mv 4_mpp/4_mpp.pdf $@
docs/5a_clearcode.pdf: 5a_clearcode/5a_clearcode.tex latex/header.tex
cd 5a_clearcode;xelatex 5a_clearcode
mv 5a_clearcode/5a_clearcode.pdf $@
docs/5a_clearcode_withnotes.pdf: 5a_clearcode/5a_clearcode_withnotes.tex latex/header.tex
cd 5a_clearcode;xelatex 5a_clearcode_withnotes
cd 5a_clearcode;pdfnup 5a_clearcode_withnotes.pdf --nup 1x2 --no-landscape --paper letterpaper --frame true --scale 0.9
mv 5a_clearcode/5a_clearcode_withnotes-nup.pdf $@
5a_clearcode/5a_clearcode_withnotes.tex: 5a_clearcode/5a_clearcode.tex
ruby/createVersionWithNotes.rb $< $@
docs/5b_rpack.pdf: 5b_packages/5b_rpack.tex latex/header.tex
cd 5b_packages;xelatex 5b_rpack
mv 5b_packages/5b_rpack.pdf $@
docs/5b_rpack_withnotes.pdf: 5b_packages/5b_rpack_withnotes.tex latex/header.tex
cd 5b_packages;xelatex 5b_rpack_withnotes
cd 5b_packages;pdfnup 5b_rpack_withnotes.pdf --nup 1x2 --no-landscape --paper letterpaper --frame true --scale 0.9
mv 5b_packages/5b_rpack_withnotes-nup.pdf $@
5b_packages/5b_rpack_withnotes.tex: 5b_packages/5b_rpack.tex
ruby/createVersionWithNotes.rb $< $@