add some makefile templates

diff --git a/templates/makefiles/gene_information.mk b/templates/makefiles/gene_information.mk
new file mode 100644 (file)
index 0000000..086894e
--- /dev/null
+++ b/templates/makefiles/gene_information.mk
@@ -0,0 +1,6 @@
+GENE_INFO ?=$(shell dir=./; while [ "$$( (cd $${dir} >/dev/null; pwd) )" != "/" ]; do if [ -e "$${dir}bin/gene_info" ]; then echo $${dir}bin/gene_info; break; fi; dir="$${dir}../"; done;)
+
+GENE_INFO_OPTIONS ?= --splicing
+
+gene_information.txt: gene_list.txt $(GENE_INFO) 
+               $(GENE_INFO) $(GENE_INFO_OPTIONS) $< > $@;

diff --git a/templates/makefiles/snp_information.mk b/templates/makefiles/snp_information.mk
new file mode 100644 (file)
index 0000000..8a89c6b
--- /dev/null
+++ b/templates/makefiles/snp_information.mk
@@ -0,0 +1,9 @@
+SNP_INFO ?=$(shell dir=./; while [ "$$( (cd $${dir} >/dev/null; pwd) )" != "/" ]; do if [ -e "$${dir}bin/snp_info" ]; then echo $${dir}bin/snp_info; break; fi; dir="$${dir}../"; done;)
+
+snp_information.txt: snp_list.txt
+       if [ -e $@.target.md5sum ] && [ -e $@ ] && md5sum --status --check $@.target.md5sum; then \
+               touch $@; \
+       else \
+               $(SNP_INFO) $(SNP_INFO_OPTIONS) $< > $@; \
+               md5sum $^ > $@.target.md5sum; \
+       fi;

diff --git a/templates/makefiles/sweave_rules.mk b/templates/makefiles/sweave_rules.mk
new file mode 100644 (file)
index 0000000..32b1a44
--- /dev/null
+++ b/templates/makefiles/sweave_rules.mk
@@ -0,0 +1,15 @@
+R ?= R
+
+%.pdf: %.svg
+       inkscape -A $@ $<
+       pdfcrop $@
+       mv $(dir $@)*-crop.pdf $@
+
+%.png: %.svg
+       inkscape -e $@ -d 300 $<
+
+%.tex: %.Rnw
+       $(R) CMD Sweave --encoding=utf-8 $<
+
+%.pdf: %.tex $(wildcard *.bib) $(wildcard *.tex)
+       latexmk -pdflatex=xelatex -bibtex -use-make -pdf $<