From c9b5f20812fae3bcbdf3ee194c06e7b9f574cc70 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Fri, 12 May 2017 08:43:15 -0700
Subject: [PATCH] add some makefile templates

---
 templates/makefiles/gene_information.mk |  6 ++++++
 templates/makefiles/snp_information.mk  |  9 +++++++++
 templates/makefiles/sweave_rules.mk     | 15 +++++++++++++++
 3 files changed, 30 insertions(+)
 create mode 100644 templates/makefiles/gene_information.mk
 create mode 100644 templates/makefiles/snp_information.mk
 create mode 100644 templates/makefiles/sweave_rules.mk

diff --git a/templates/makefiles/gene_information.mk b/templates/makefiles/gene_information.mk
new file mode 100644
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="$${dir}../"; done;)
+
+GENE_INFO_OPTIONS ?= --splicing
+
+gene_information.txt: gene_list.txt $(GENE_INFO) 
+	    	$(GENE_INFO) $(GENE_INFO_OPTIONS) $< > $@;
diff --git a/templates/makefiles/snp_information.mk b/templates/makefiles/snp_information.mk
new file mode 100644
index 0000000..8a89c6b
--- /dev/null
+++ b/templates/makefiles/snp_information.mk
@@ -0,0 +1,9 @@
+SNP_INFO ?=$(shell dir=./; while [ "$$( (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
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 $<
-- 
2.39.2