X-Git-Url: https://git.donarmstrong.com/?p=using_make_for_science.git;a=blobdiff_plain;f=using_make_for_science.Rnw;h=2fee8e94ee34bcf3f56847ca8f9112ef4054a53d;hp=9fd424a3eb6ce1d2514644c519653b8815cfd3fa;hb=HEAD;hpb=2b141c12e69485e71e36649c8128a28deddcf373

diff --git a/using_make_for_science.Rnw b/using_make_for_science.Rnw
index 9fd424a..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}}
 }
@@ -147,8 +147,8 @@
   \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
@@ -200,8 +200,8 @@ 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}.
+  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}{$^} -- all prerequisites %$
@@ -214,7 +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
@@ -271,7 +271,7 @@ clean:
 
 \begin{frame}[fragile]{Special Targets}
 \begin{minted}[showtabs]{make}
-%.fasta.gz: %.fasta
+%.fasta: %.fasta.gz
 	gzip -dc $< > $@
 
 %.bam: %.sam
@@ -421,6 +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}