From 85b7c5cb2963238e3b4de1bc8228130eb4295e97 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 26 May 2015 09:16:16 -0700
Subject: [PATCH] add fpkm script

---
 fpkm_from_srr | 45 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100755 fpkm_from_srr

diff --git a/fpkm_from_srr b/fpkm_from_srr
new file mode 100755
index 0000000..e30372a
--- /dev/null
+++ b/fpkm_from_srr
@@ -0,0 +1,45 @@
+#!/bin/bash
+# PBS -M id -un
+
+CORES=8
+MAX_MEM=32
+
+
+function actually_run_the_alignment {
+    module load sratoolkit/2.3.5-2;
+    module load bwa/0.7.10;
+    module load cufflinks/2.2.1;
+    (cd $SRR;
+     fastq-dump ${SRR}.sra;
+     bwa mem -t ${CORES} $REF ${SRR}.fastq.gz | samtools view -b -o ${SRR}.bam;
+     samtools sort ${SRR}.bam -o ${SRR}.sorted.bam -T temp
+     cufflinks -p ${MAX_MEM} -G $GTF ${SRR}.sorted.bam;
+     rm -f ${SRR}.fastq.gz ${SRR}.bam
+    );
+};
+
+function set_up_the_run {
+    FROM_SRR_SRR=$1
+    FROM_SRR_REF=$2
+    FROM_SRR_GTF=$3
+    export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
+    mkdir -p $SRR;
+    (cd $SRR;
+     wget -O ${SRR}.sra ftp://ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/${SRR:0:6}/${SRR}/${SRR}.sra;
+    );
+    qsub -q budget -v FROM_SRR_SRR,FROM_SRR_GTF,FROM_SRR_REF -S /bin/bash -d $(pwd) -M donarm@illinois.edu -l "nodes=1:ppn=${CORES},mem=${MAX_MEM}" "$0"    
+};
+
+
+if [ -z "$1" ] || [ -z "$2"] || [ -z "$3" ]; then
+    if [ -z "$FROM_SRR_SRR" ]; then
+        actually_run_the_alignment;
+        exit 0;
+    fi;
+else
+    set_up_the_run;
+    exit 0;
+fi;
+echo "You need to give an SRR, REF, and GTF on the command line";
+exit 1;
+
-- 
2.39.2