if one wishes to generate the html via make, I added the makefile.

data/Makefile

@@ -0,0 +1,18 @@
+.PHONY: all
+
+OUTPUTS = tmrc.simg
+
+cpm:
+	mkdir -p cpm/3_cali_and_tumaco cpm/4_cali cpm/4_tumaco excel figures rda rpkm
+
+preprocessing/TMRC30001:
+	cd preprocessing && tar xaf pruned_counts_host.tar
+	cd preprocessing && tar xaf pruned_counts_parasite.tar
+	cd preprocessing && tar xaf scott_counts.tar
+
+%.render: %.Rmd cpm preprocessing/TMRC30001
+	Rscript -e "hpgltools::renderme('$<', 'html_document')" \
+		2>&1 | tee $(basename $<).stdout
+
+%.edit:	%.Rmd
+	emacs -nw $<.Rmd