X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/bcb686d8a83a3659783bcbdbf9a0e559246eeb61..HEAD:/Makefile

diff --git a/Makefile b/Makefile
index 1407962..09d2d34 100644
--- a/Makefile
+++ b/Makefile
@@ -32,7 +32,7 @@ endif
 
 
 # Controls
-.PHONY : commands clean files install-rmd-deps
+.PHONY : commands clean files
 
 # Default target
 .DEFAULT_GOAL := commands
@@ -93,10 +93,10 @@ workshop-check :
 ## III. Commands specific to lesson websites
 ## =================================================
 
-.PHONY : lesson-check lesson-md lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme install-rmd-deps
 
 # RMarkdown files
-RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
+RMD_SRC = $(wildcard _episodes_rmd/*.Rmd)
 RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
 
 # Lesson source files in the order they appear in the navigation menu.
@@ -107,7 +107,8 @@ MARKDOWN_SRC = \
   $(sort $(wildcard _episodes/*.md)) \
   reference.md \
   $(sort $(wildcard _extras/*.md)) \
-  LICENSE.md
+  LICENSE.md \
+  CONTRIBUTING.md
 
 # Generated lesson files in the order they appear in the navigation menu.
 HTML_DST = \
@@ -115,18 +116,18 @@ HTML_DST = \
   ${DST}/conduct/index.html \
   ${DST}/setup/index.html \
   $(patsubst _episodes/%.md,${DST}/%/index.html,$(sort $(wildcard _episodes/*.md))) \
-  ${DST}/reference/index.html \
+  ${DST}/reference.html \
   $(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \
   ${DST}/license/index.html
 
 ## * install-rmd-deps : Install R packages dependencies to build the RMarkdown lesson
 install-rmd-deps:
-	Rscript -e 'source("bin/dependencies.R"); install_dependencies(identify_dependencies())'
+	@${SHELL} bin/install_r_deps.sh
 
 ## * lesson-md        : convert Rmarkdown files to markdown
 lesson-md : ${RMD_DST}
 
-_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-dependencies
+_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-deps
 	@mkdir -p _episodes
 	@bin/knit_lessons.sh $< $@