X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=using_make_for_science.Rnw;h=2fee8e94ee34bcf3f56847ca8f9112ef4054a53d;hb=a58898c9eb5ffe7aad59a60ea46ee121154440dd;hp=8ff99d10871fb6470e71e3d43a677c3f6518bc0e;hpb=965452df6fbe769c2733543b8880db096a1fb850;p=using_make_for_science.git

diff --git a/using_make_for_science.Rnw b/using_make_for_science.Rnw
index 8ff99d1..2fee8e9 100644
--- a/using_make_for_science.Rnw
+++ b/using_make_for_science.Rnw
@@ -77,7 +77,7 @@
   \setbeamercolor*{fine separation line}{}
   \setbeamercovered{transparent}  
   \logo{\begin{tikzpicture}% Pale figure
-      {\node[opacity=0.7]{\IfFileExists{./logo.pdf}{\includegraphics[height=1.5cm]{logo.pdf}}{}%
+      {\node[opacity=0.7]{\IfFileExists{./logo.pdf}{\includegraphics[height=1cm,width=1cm,keepaspectratio]{logo.pdf}}{}%
         };}%
     \end{tikzpicture}}
 }
@@ -89,6 +89,8 @@
 \subject{make for science}
 \begin{document}
 
+\IfFileExists{./relevant_xkcd.png}{\frame[plain]{\centering \includegraphics[width=\textwidth,height=\textheight,keepaspectratio]{./relevant_xkcd.png}}}
+
 \frame[plain]{\titlepage}
 
 \mode<article>{\maketitle}
@@ -145,12 +147,12 @@
   \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 Large community -- lots of people use GNU make. It's not going
+    to go away tomorrow.
   \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;}
+    going to run fairly easily: \mintinline{shell}{make -n target;}
   \item Parallel -- make can make targets in parallel:
     \mintinline{shell}{make -j8 all;}
   \item Language agnostic -- make doesn't care what language your code
@@ -198,9 +200,9 @@ TARGETS: PREREQUISITES
     value is assigned at the moment the variable is created
   \end{itemize}
 \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}{$@} -- tgt name %$
+  the command line: \mintinline{shell}{FOO=blah make} or
+  \mintinline{shell}{make FOO=bleargh}.
+\item \mintinline{make}{$@} -- target name %$
 \item \mintinline{make}{$*} -- current stem %$ 
 \item \mintinline{make}{$^} -- all prerequisites %$
 \item \mintinline{make}{$<} -- first prerequisite %$
@@ -212,7 +214,7 @@ TARGETS: PREREQUISITES
 
 \begin{frame}[fragile]{Some Functions}
   \begin{itemize}
-  \item \mintinline{make}{$(patsubst %.bam,%.sam,foo.sam bar.sam)} %$
+  \item \mintinline{make}{$(patsubst %.sam,%.bam,foo.sam bar.sam)} %$
       -- returns foo.bam bar.bam.
   \item \mintinline{make}{$(filter-out %.bam,foo.sam bar.bam)} %$
       -- returns foo.sam
@@ -230,17 +232,17 @@ TARGETS: PREREQUISITES
 
 \begin{frame}[fragile]{How does make know what to build?}
 \begin{minted}[showtabs]{make}
-first_tgt: 
+first_target: 
 	touch $@
-second_tgt: first_tgt
+second_target: first_target
 	touch $@
 \end{minted}
   \begin{itemize}
-  \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}
+  \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}
   \end{itemize}
 \end{frame}
 
@@ -252,12 +254,12 @@ second_tgt: first_tgt
 .PHONY: clean
 
 clean:
-	rm -f first_tgt second_tgt
+	rm -f first_target second_target
 \end{minted}
   \begin{itemize}
   \item \mintinline{make}{.PHONY} -- any time make considers this
-    tgt, it is run unconditionally, even if a file exists.
-  \item \mintinline{make}{.ONESHELL} -- when a tgt is built, all
+    target, it is run unconditionally, even if a file exists.
+  \item \mintinline{make}{.ONESHELL} -- when a target 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}
@@ -269,7 +271,7 @@ clean:
 
 \begin{frame}[fragile]{Special Targets}
 \begin{minted}[showtabs]{make}
-%.fasta.gz: %.fasta
+%.fasta: %.fasta.gz
 	gzip -dc $< > $@
 
 %.bam: %.sam
@@ -288,9 +290,12 @@ clean:
 \subsection{This Presentation}
 
 \begin{frame}[fragile]{How this presentation is made}
-\inputminted[showtabs]{make}{Makefile}
+\inputminted[showtabs,breaklines,firstline=3]{make}{Makefile}
+\end{frame}
+\begin{frame}[fragile]{How this presentation is made}
   \begin{itemize}
-  \item all is the default tgt
+  \item all is the default 
+  \item Download the optional relevant\_xkcd.png
   \item Make .tex files from the knitr source.
   \item The third rule uses latexmk to build the pdf using \XeLaTeX.
   \end{itemize}
@@ -335,7 +340,17 @@ FASTQ_FILES:=$(patsubst %,%_1.fastq.gz,$(SRRS))  $(patsubst %,%_2.fastq.gz,$(SRR
 endif
 
 make_fastq: $(FASTQ_FILES)
+\end{minted}
+%$
+\begin{itemize}
+\item Use ifeq/else/endif to handle paired reads differently from
+  unpaired reads
+\item FASTQ\_FILES is the full set of fastq files dumped from the SRAs.
+\end{itemize}
+\end{frame}
 
+\begin{frame}[fragile]{Calling records from SRA: Dumping fastq #2}
+\begin{minted}[showtabs,breaklines]{make}
 ifeq ($(NREADS),1)
 $(FASTQ_FILES): %.fastq.gz: %.sra
 else
@@ -346,8 +361,8 @@ endif
 \end{minted}
 %$
   \begin{itemize}
-  \item Call fastq-dump to dump the fastq files
   \item Handles NREADS of 1 and 2 differently
+  \item Call fastq-dump to dump the fastq files
   \end{itemize}
 \end{frame}
 
@@ -406,6 +421,8 @@ $(SRX)_genes.fpkm_tracking: $(SRX)_star.bam $(BOWTIE_INDEX_DIR)$(GTF)
   \begin{itemize}
   \item Timestamps, not MD5sums
   \item Complicated workflows
+  \item Interaction of rules can be complicated to understand
+  \item Yet Another Language
   \end{itemize}
 \end{frame}
 
@@ -434,12 +451,17 @@ TARGET: PREREQ1 PREREQ1
 
 \subsection{Complicated Workflows}
 
-\begin{frame}{What about complicated workflows?}
+\begin{frame}[fragile]{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}
+  \begin{minted}[showtabs,breaklines]{make}
+complicated_workflow_done: req1 req2 req3
+	./complicated_workflow.sh $^;
+	touch $@;
+\end{minted}
 \end{frame}
 
 \section{Further Resources}