add empty slides for the last few bits that I want to talk about

diff --git a/using_make_for_science.Rnw b/using_make_for_science.Rnw
index f418d490cc5469f5e1a98d21f88295d5c410ccfe..4e0ae036915988317ebc8e1a3fcabf37265ad0ef 100644 (file)
--- a/using_make_for_science.Rnw
+++ b/using_make_for_science.Rnw
@@ -336,13 +336,13 @@ $(SRX)_star.bam:
        $(MODULE) load STAR/2.4.2a; \
        mkdir -p $(SRX)_star; \
        STAR --outFileNamePrefix $(SRX)_star/ \
-               --outSAMtype BAM SortedByCoordinate \
-               --runThreadN $(CORES) \
-        --outSAMstrandField intronMotif \
-               --genomeDir $(STAR_INDEX_DIR) \
-               --readFilesCommand "gzip -dc" \
-               --readFilesIn $(TOPHAT_FASTQ_ARGUMENT);
-       ln $(SRX)_star/Aligned.sortedByCoord.out.bam $@ -s
+       --outSAMtype BAM SortedByCoordinate \
+       --runThreadN $(CORES) \
+       --outSAMstrandField intronMotif \
+       --genomeDir $(STAR_INDEX_DIR) \
+       --readFilesCommand "gzip -dc" \
+       --readFilesIn $(TOPHAT_FASTQ_ARGUMENT);
+       ln $(SRX)_star/Aligned.*.bam $@ -s
 \end{minted} %$
   \begin{itemize}
   \item Call STAR with lots of options to do the alignment
@@ -366,24 +366,45 @@ $(SRX)_genes.fpkm_tracking: $(SRX)_star.bam $(BOWTIE_INDEX_DIR)$(GTF)
 \end{frame}
 
 \begin{frame}[fragile]{Run it on biocluster}
-  \begin{minted}[shell]
+  \begin{minted}{shell}
 for a in SRX*/Makefile; do 
    (cd $(dirname $a); 
-    MAKE_TARGET=call qsub -q default -v MAKE_TARGET -S /bin/bash \
-      -d "$(pwd)" -l "nodes=1:ppn=8,mem=12G" \
+    MAKE_TARGET=call qsub -q default \
+      -v MAKE_TARGET -S /bin/bash \
+      -d "$(pwd)" -l "nodes=1:ppn=8,mem=70G" \
       ~donarm/uiuc_igb_scripts/run_make
     );
 done;
 \end{minted} %$
+\begin{itemize}
+\item Use qsub and some shell scripting to run everything
+\item Uses a special script which calls make with a specific target
+\end{itemize}
 \end{frame}
 
 \section{Why not make?}
 
+\begin{frame}{Why not make?}
+  \begin{itemize}
+  \item Timestamps, not MD5sums
+  \item Complicated workflows
+  \end{itemize}
+\end{frame}
+
 \subsection{Timestamps}
 
+\begin{frame}{Dealing with timestamps}
+\end{frame}
+
 \subsection{Complicated Workflows}
 
+\begin{frame}{Complicated Workflow}
+  
+\end{frame}
+
 \section{Further Resources}
 
+\begin{frame}{Further Resources}
+\end{frame}
 
 \end{document}