more changes to makefile presentation

diff --git a/using_make_for_science.Rnw b/using_make_for_science.Rnw
index 29df3764fdd518e8ea610cde87bc363646b76fc9..8ff99d10871fb6470e71e3d43a677c3f6518bc0e 100644 (file)
--- a/using_make_for_science.Rnw
+++ b/using_make_for_science.Rnw
@@ -133,12 +133,31 @@
   \item Gradle (Rake DSL)
   \item Leiningen (Clojure)
   \item Tweaker (task definitions in any language)
   \item Gradle (Rake DSL)
   \item Leiningen (Clojure)
   \item Tweaker (task definitions in any language)

+  \item Ruffus (Pipeline library for python)

   \item
     \href{https://en.wikipedia.org/wiki/List_of_build_automation_software}{Wikipedia
       List of build automation software}
   \end{itemize}
 \end{frame}
 
   \item
     \href{https://en.wikipedia.org/wiki/List_of_build_automation_software}{Wikipedia
       List of build automation software}
   \end{itemize}
 \end{frame}
 

+\subsection{Why use GNU make?}
+\begin{frame}{Why use GNU make?}
+  \begin{itemize}
+  \item Ubiquitous -- any machine which you can run command line tools
+    on has GNU make available.
+  \item Large community -- lots of people use GNU make. It's well
+    understood and you can get questions answered
+  \item Simple rules -- all of the rules are in a simple text file
+    which is easily edited and version controlled
+  \item Reasonable debugging -- you can see the commands that make is
+    going to run fairly easily: \mintinline{shell}{make -n tgt;}
+  \item Parallel -- make can make targets in parallel:
+    \mintinline{shell}{make -j8 all;}
+  \item Language agnostic -- make doesn't care what language your code
+    is written in
+  \end{itemize}
+\end{frame}
+

 \section{Introduction to Makefiles}
 
 \begin{frame}[fragile]{Simple Makefile}
 \section{Introduction to Makefiles}
 
 \begin{frame}[fragile]{Simple Makefile}


@@ -181,7 +200,7 @@ TARGETS: PREREQUISITES
 \item Variables can come from the environment and can be overridden on
   the command line: \mintinline{shell}{make FOO=bleargh} or
   \mintinline{shell}{FOO=blah make}.
 \item Variables can come from the environment and can be overridden on
   the command line: \mintinline{shell}{make FOO=bleargh} or
   \mintinline{shell}{FOO=blah make}.

-\item \mintinline{make}{$@} -- target name %$
+\item \mintinline{make}{$@} -- tgt name %$

 \item \mintinline{make}{$*} -- current stem %$ 
 \item \mintinline{make}{$^} -- all prerequisites %$
 \item \mintinline{make}{$<} -- first prerequisite %$
 \item \mintinline{make}{$*} -- current stem %$ 
 \item \mintinline{make}{$^} -- all prerequisites %$
 \item \mintinline{make}{$<} -- first prerequisite %$


@@ -211,17 +230,17 @@ TARGETS: PREREQUISITES
 
 \begin{frame}[fragile]{How does make know what to build?}
 \begin{minted}[showtabs]{make}
 
 \begin{frame}[fragile]{How does make know what to build?}
 \begin{minted}[showtabs]{make}

-first_target: 
+first_tgt: 

        touch $@
        touch $@

-second_target: first_target
+second_tgt: first_tgt

        touch $@
 \end{minted}
   \begin{itemize}
        touch $@
 \end{minted}
   \begin{itemize}

-  \item By default, make builds the first target.
-  \item You can specify a specific target to build on the command line
-    (\mintinline{shell}{make first_target}).
-  \item You can change the default target by using the variable
-    \mintinline{make}{.DEFAULT_GOAL := second_target}
+  \item By default, make builds the first tgt.
+  \item You can specify a specific tgt to build on the command line
+    (\mintinline{shell}{make first_tgt}).
+  \item You can change the default tgt by using the variable
+    \mintinline{make}{.DEFAULT_GOAL := second_tgt}

   \end{itemize}
 \end{frame}
 
   \end{itemize}
 \end{frame}
 


@@ -233,12 +252,12 @@ second_target: first_target
 .PHONY: clean
 
 clean:
 .PHONY: clean
 
 clean:

-       rm -f first_target second_target
+       rm -f first_tgt second_tgt

 \end{minted}
   \begin{itemize}
   \item \mintinline{make}{.PHONY} -- any time make considers this
 \end{minted}
   \begin{itemize}
   \item \mintinline{make}{.PHONY} -- any time make considers this

-    target, it is run unconditionally, even if a file exists.
-  \item \mintinline{make}{.ONESHELL} -- when a target is built, all
+    tgt, it is run unconditionally, even if a file exists.
+  \item \mintinline{make}{.ONESHELL} -- when a tgt is built, all

     lines will be given to a single invocation of the shell.
   \item Lots of other special targets which are not described here.
   \end{itemize}
     lines will be given to a single invocation of the shell.
   \item Lots of other special targets which are not described here.
   \end{itemize}


@@ -271,7 +290,7 @@ clean:
 \begin{frame}[fragile]{How this presentation is made}
 \inputminted[showtabs]{make}{Makefile}
   \begin{itemize}
 \begin{frame}[fragile]{How this presentation is made}
 \inputminted[showtabs]{make}{Makefile}
   \begin{itemize}

-  \item all is the default target
+  \item all is the default tgt

   \item Make .tex files from the knitr source.
   \item The third rule uses latexmk to build the pdf using \XeLaTeX.
   \end{itemize}
   \item Make .tex files from the knitr source.
   \item The third rule uses latexmk to build the pdf using \XeLaTeX.
   \end{itemize}


@@ -290,7 +309,7 @@ clean:
 \begin{frame}[fragile]{Calling records from SRA: Downloading}
 \begin{minted}[showtabs,breaklines]{make}
 SRX=SRX007165
 \begin{frame}[fragile]{Calling records from SRA: Downloading}
 \begin{minted}[showtabs,breaklines]{make}
 SRX=SRX007165

-SRRS=SRR020291 SRR020290 SRR020288 SRR020287 SRR020289
+SRRS=SRR020291 SRR020290

 NREADS=1
 SRR_FILES=$(patsubst %,%.sra,$(SRRS))
 
 NREADS=1
 SRR_FILES=$(patsubst %,%.sra,$(SRRS))
 


@@ -298,7 +317,8 @@ get_srr: $(SRR_FILES)
 
 $(SRR_FILES): %.sra:
        rsync -avP "rsync://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/$(shell echo -n $*|sed 's/\(SRR[0-9][0-9][0-9]\).*/\1/')/$*/$*.sra" $@;
 
 $(SRR_FILES): %.sra:
        rsync -avP "rsync://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/$(shell echo -n $*|sed 's/\(SRR[0-9][0-9][0-9]\).*/\1/')/$*/$*.sra" $@;

-\end{minted} %$
+\end{minted}
+%$

   \begin{itemize}
   \item First three lines are actually generated by other code and
     included
   \begin{itemize}
   \item First three lines are actually generated by other code and
     included


@@ -323,7 +343,8 @@ else
 endif
        $(MODULE) load sratoolkit/2.3.5-2; \
        fastq-dump --split-3 --gzip $^;
 endif
        $(MODULE) load sratoolkit/2.3.5-2; \
        fastq-dump --split-3 --gzip $^;

-\end{minted} %$
+\end{minted}
+%$

   \begin{itemize}
   \item Call fastq-dump to dump the fastq files
   \item Handles NREADS of 1 and 2 differently
   \begin{itemize}
   \item Call fastq-dump to dump the fastq files
   \item Handles NREADS of 1 and 2 differently


@@ -343,7 +364,8 @@ $(SRX)_star.bam:
        --readFilesCommand "gzip -dc" \
        --readFilesIn $(TOPHAT_FASTQ_ARGUMENT);
        ln $(SRX)_star/Aligned.*.bam $@ -s
        --readFilesCommand "gzip -dc" \
        --readFilesIn $(TOPHAT_FASTQ_ARGUMENT);
        ln $(SRX)_star/Aligned.*.bam $@ -s

-\end{minted} %$
+\end{minted}
+%$

   \begin{itemize}
   \item Call STAR with lots of options to do the alignment
   \end{itemize}
   \begin{itemize}
   \item Call STAR with lots of options to do the alignment
   \end{itemize}


@@ -359,7 +381,8 @@ $(SRX)_genes.fpkm_tracking: $(SRX)_star.bam $(BOWTIE_INDEX_DIR)$(GTF)
        for file in genes.fpkm_tracking isoforms.fpkm_tracking skipped.gtf transcripts.gtf; do \
                mv $${file} $(SRX)_$${file}; \
        done;
        for file in genes.fpkm_tracking isoforms.fpkm_tracking skipped.gtf transcripts.gtf; do \
                mv $${file} $(SRX)_$${file}; \
        done;

-\end{minted} %$
+\end{minted}
+%$

   \begin{itemize}
   \item Use cufflinks to call
   \end{itemize}
   \begin{itemize}
   \item Use cufflinks to call
   \end{itemize}


@@ -388,35 +411,47 @@ $(SRX)_genes.fpkm_tracking: $(SRX)_star.bam $(BOWTIE_INDEX_DIR)$(GTF)
 
 \subsection{Timestamps}
 
 
 \subsection{Timestamps}
 

-\begin{frame}{Dealing with timestamps}
-  \begin{itemize}
-  \item Make builds things on the basis of timestamps
-  \item But what if the contents haven't changed and it's expensive to
-    rebuild?
-  \item Use md5sum!
-  \end{itemize}
-\begin{minted}[showtabs,breaklines]{make}
+\begin{frame}[fragile]{Dealing with timestamps}
+  \begin{minted}[showtabs,breaklines]{make}

 TARGET: PREREQ1 PREREQ1
 TARGET: PREREQ1 PREREQ1

-       if [ -e $@.target.md5sum ] && [ -e $@ ] && \
-       md5sum --status --check $@.target.md5sum; \
-    then \
+       if [ -e $@.tgt.md5sum ] && [ -e $@ ] \
+          && md5sum --status --check \
+          $@.tgt.md5sum; then \

         touch $@; \
        else \
         touch $@; \
        else \

-           RECIPE FOR $@; \
-               md5sum $^ > $@.target.md5sum; \
+        RECIPE FOR $@; \
+        md5sum $^ > $@.tgt.md5sum; \

        fi;
 \end{minted}
        fi;
 \end{minted}

+% $
+\begin{itemize}
+\item Make builds things on the basis of timestamps
+\item But what if the contents haven't changed and it's expensive to
+  rebuild?
+\item Use md5sum!
+\end{itemize}

 \end{frame}
 
 \subsection{Complicated Workflows}
 
 \end{frame}
 
 \subsection{Complicated Workflows}
 

-\begin{frame}{Complicated Workflow}
-  
+\begin{frame}{What about complicated workflows?}
+  \begin{itemize}
+  \item If your workflow is really complicated, what then?
+  \item Use some other language to write your workflow in
+  \item Use a simple makefile which just runs the workflow
+  \end{itemize}

 \end{frame}
 
 \section{Further Resources}
 
 \begin{frame}{Further Resources}
 \end{frame}
 
 \section{Further Resources}
 
 \begin{frame}{Further Resources}

+  \begin{itemize}
+  \item GNU Make Manual: \url{https://www.gnu.org/software/make/manual/}
+  \item Mailing lists: \url{http://www.gnu.org/software/make/}
+  \item Stack overflow: \url{http://stackoverflow.com/questions/tagged/make}
+  \item Myself: \href{mailto:don@donarmstrong.com}{don@donarmstrong.com}
+  \item This presentation: \url{http://git.donarmstrong.com/using\_make\_for\_science.git}
+  \end{itemize}

 \end{frame}
 
 \end{document}
 \end{frame}
 
 \end{document}