From 3d57e6f489bbe652663fc90769ef5935c97b7934 Mon Sep 17 00:00:00 2001
From: Arun Seetharam <arnstrm@iastate.edu>
Date: Thu, 8 Mar 2018 10:15:11 -0600
Subject: [PATCH] added new scripts and modified histat2 to check completion of
 steps before proceeding

---
 runAlignmentStats.sh |  2 +-
 runHISAT2.sh         | 29 ++++++++++++++++++-----------
 2 files changed, 19 insertions(+), 12 deletions(-)

diff --git a/runAlignmentStats.sh b/runAlignmentStats.sh
index 46dc537..a7de85b 100755
--- a/runAlignmentStats.sh
+++ b/runAlignmentStats.sh
@@ -20,7 +20,7 @@ fi
 
 module load R
 module load java
-module load picard
+module load picard/2.9.0
 module load samtools
 module load GIF/qualimap
 
diff --git a/runHISAT2.sh b/runHISAT2.sh
index 1001c50..b9b74c1 100755
--- a/runHISAT2.sh
+++ b/runHISAT2.sh
@@ -1,21 +1,28 @@
 #!/bin/bash
-
 module load hisat2
 module load samtools
-DBDIR="/data013/GIF/arnstrm/GENOMEDB"
-GENOME="Mus_musculus.GRCm38.dna.toplevel_hisat2"
-
+DBDIR="/work/GIF/arnstrm/GENOMEDB"
+GENOME="$1"
+#GENOME="TAIR10"
 p=16
-R1_FQ="$1"
-R2_FQ="$2"
-
+R1_FQ="$2"
+R2_FQ="$3"
 OUTPUT=$(basename ${R1_FQ} |cut -f 1 -d "_");
-
 hisat2 \
   -p ${p} \
   -x ${DBDIR}/${GENOME} \
   -1 ${R1_FQ} \
   -2 ${R2_FQ} \
-  -S  ${OUTPUT}.sam &> ${OUTPUT}.log
-samtools view --threads 16 -b -o ${OUTPUT}.bam ${OUTPUT}.sam
-samtools sort -m 7G -o ${OUTPUT}_sorted.bam -T ${OUTPUT}_temp --threads 16 ${OUTPUT}.bam
+  -S  ${OUTPUT}.sam &> ${OUTPUT}.log || {
+echo >&2 "hisat2 alignment failed for ${OUTPUT}"
+exit 1
+}
+samtools view --threads 16 -b -o ${OUTPUT}.bam ${OUTPUT}.sam  || {
+echo >&2 "sam to bam conversion failed for ${OUTPUT}"
+exit 1
+}
+samtools sort -m 4G -o ${OUTPUT}_sorted.bam -T ${OUTPUT}_temp --threads 16 ${OUTPUT}.bam || {
+echo >&2 "sorting bam failed for ${OUTPUT}"
+exit 1
+}
+