/
Makefile
99 lines (74 loc) · 3.39 KB
/
Makefile
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all: pdf
PDFS = BCFv1_qref.pdf \
BCFv2_qref.pdf \
$(if $(CIRCLECI),,BEDv1.pdf) \
CRAMv2.1.pdf \
CRAMv3.pdf \
crypt4gh.pdf \
CRAMcodecs.pdf \
CSIv1.pdf \
SAMv1.pdf \
SAMtags.pdf \
tabix.pdf \
VCFv4.1.pdf \
VCFv4.2.pdf \
VCFv4.3.pdf \
VCFv4.4.pdf \
VCFv4.5.draft.pdf
pdf: $(PDFS:%=new/%)
%.pdf: new/%.pdf
cp $^ $@
new/BEDv1.pdf diff/BEDv1.pdf: BEDv1.tex new/BEDv1.ver
new/CRAMv2.1.pdf diff/CRAMv2.1.pdf: CRAMv2.1.tex new/CRAMv2.1.ver
new/CRAMv3.pdf diff/CRAMv3.pdf: CRAMv3.tex new/CRAMv3.ver
new/crypt4gh.pdf diff/crypt4gh.pdf: crypt4gh.tex new/crypt4gh.ver
new/SAMv1.pdf diff/SAMv1.pdf: SAMv1.tex new/SAMv1.ver
new/SAMtags.pdf diff/SAMtags.pdf: SAMtags.tex new/SAMtags.ver
new/VCFv4.1.pdf diff/VCFv4.1.pdf: VCFv4.1.tex new/VCFv4.1.ver
new/VCFv4.2.pdf diff/VCFv4.2.pdf: VCFv4.2.tex new/VCFv4.2.ver
new/VCFv4.3.pdf diff/VCFv4.3.pdf: VCFv4.3.tex new/VCFv4.3.ver
new/VCFv4.4.pdf diff/VCFv4.4.pdf: VCFv4.4.tex new/VCFv4.4.ver
new/VCFv4.5.draft.pdf diff/VCFv4.5.draft.pdf: VCFv4.5.draft.tex new/VCFv4.5.draft.ver
new/CRAMcodecs.pdf diff/CRAMcodecs.pdf: CRAMcodecs.tex new/CRAMcodecs.ver
# Set LATEXMK to "scripts/rerun.sh new/$* $(PDFLATEX)" to use the previous
# controller script, e.g., if your installation does not have latexmk.
PDFLATEX = pdflatex
LATEXMK = latexmk $(LATEXMK_ENGINE) $(LATEXMK_FLAGS)
LATEXMK_ENGINE = --pdf --pdflatex='$(PDFLATEX)'
LATEXMK_FLAGS =
LATEXDIFF_ENGINE = --config LATEX=pdflatex
new/%.pdf: %.tex | new
$(LATEXMK) --output-directory=new $<
new/BEDv1.pdf: LATEXMK_ENGINE = --lualatex
new/CRAMv2.1.ver new/CRAMv3.ver: img/CRAMFileFormat2-1-fig001.png img/CRAMFileFormat2-1-fig002.png img/CRAMFileFormat2-1-fig003.png img/CRAMFileFormat2-1-fig004.png img/CRAMFileFormat2-1-fig005.png img/CRAMFileFormat2-1-fig006.png img/CRAMFileFormat2-1-fig007.png
new/VCFv4.1.ver new/VCFv4.2.ver new/VCFv4.3.ver new/VCFv4.4.ver: img/all_orientations-400x296.png img/derivation-400x267.png img/erosion-400x211.png img/inserted_contig-400x247.png img/inserted_sequence-400x189.png img/inversion-400x95.png img/microhomology-400x248.png img/multiple_mates-400x280.png img/phasing-400x259.png img/reciprocal_rearrangement-400x192.png img/telomere-400x251.png
new/CRAMcodecs.ver: img/range_code.png
new/%.ver: %.tex | new
scripts/genversion.sh $^ > $@
new:
mkdir new
diff diffs: $(PDFS:%=diff/%)
OLD = HEAD
NEW =
diff/%.pdf: %.tex
BIBINPUTS=:.. TEXINPUTS=:..:../new latexdiff-vc $(LATEXDIFF_ENGINE) --pdf --dir diff --force --git --only-changes --graphics-markup=none --ignore-warnings --revision $(OLD) $(if $(NEW),--revision $(NEW)) $<
diff/BEDv1.pdf: LATEXDIFF_ENGINE = --config LATEX=lualatex
show-styles:
@sed -n '/\\usepackage/s/.*{\(.*\)}$$/\1/p' *.tex | sort | uniq -c
mostlyclean:
-rm -f new/*.aux new/*.bbl new/*.blg new/*.fdb_latexmk new/*.fls new/*.log new/*.out new/*.toc new/*.ver
-rm -f diff/**.aux diff/*.blg diff/*.idx diff/*.log diff/*.out diff/*.tex diff/*.toc
clean: mostlyclean
-rm -f $(PDFS:%=new/%)$(if $(wildcard new),; rmdir new)
-rm -f $(PDFS:%=diff/%)$(if $(wildcard diff),; rmdir diff)
-rm -rf .jekyll-cache .jekyll-metadata _site
# Checking of MM tag perl script
check test:
cd test/SAMtags; \
for i in `echo *.sam | sed 's/\.sam//g'`; \
do \
./parse_mm.pl $$i.sam > _; \
cmp _ $$i.txt; \
done; \
rm _
.PHONY: all pdf diff diffs show-styles mostlyclean clean