From f7262f641eff7f5477fb20cbcdd69601150b74eb Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 4 Aug 2015 15:38:27 -0700
Subject: [PATCH] add empty slides for the last few bits that I want to talk
 about

---
 using_make_for_science.Rnw | 41 ++++++++++++++++++++++++++++----------
 1 file changed, 31 insertions(+), 10 deletions(-)

diff --git a/using_make_for_science.Rnw b/using_make_for_science.Rnw
index f418d49..4e0ae03 100644
--- 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}
-- 
2.39.2