Remove software carpentries logo

[rnaseq-cwl-training.git] / Makefile

diff --git a/Makefile b/Makefile
index 1407962ca27c9a35a384463d41647f304bad7e9b..09d2d3414e510b0aa6ba60959bbd328bf04979df 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -32,7 +32,7 @@ endif
 
 
 # Controls
 
 
 # Controls

-.PHONY : commands clean files install-rmd-deps
+.PHONY : commands clean files

 
 # Default target
 .DEFAULT_GOAL := commands
 
 # Default target
 .DEFAULT_GOAL := commands


@@ -93,10 +93,10 @@ workshop-check :
 ## III. Commands specific to lesson websites
 ## =================================================
 
 ## 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
 
 # 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.
 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)) \
   $(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 = \
 
 # 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}/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:
   $(patsubst _extras/%.md,${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}
 
 
 ## * 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 $< $@
 
        @mkdir -p _episodes
        @bin/knit_lessons.sh $< $@