X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=fpkm_from_srr;h=82e4ae9c3d3f860033435416d481100612876fa5;hb=e3a076b12c9216f42d6b8ae13751696fa0f3cd52;hp=27cad20bcacb01eb506f6c35ae1de0ea579d05f0;hpb=0e5f3745f8f445db4cc77967c3baa0ed25362e97;p=uiuc_igb_scripts.git

diff --git a/fpkm_from_srr b/fpkm_from_srr
index 27cad20..82e4ae9 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -1,8 +1,7 @@
 #!/bin/bash
-# PBS -M id -un
 
 CORES=8
-MAX_MEM=32
+MAX_MEM="32GB"
 
 
 function actually_run_the_alignment {
@@ -12,7 +11,7 @@ function actually_run_the_alignment {
     module load samtools/1.0;
     (cd $FROM_SRR_SRR;
      fastq-dump --gzip ${FROM_SRR_SRR}.sra;
-     bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam;
+     bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam -;
      samtools sort ${FROM_SRR_SRR}.bam -o ${FROM_SRR_SRR}.sorted.bam -T temp
      cufflinks -p ${MAX_MEM} -G $FROM_SRR_GTF ${FROM_SRR_SRR}.sorted.bam;
      rm -f ${FROM_SRR_SRR}.fastq.gz ${FROM_SRR_SRR}.bam
@@ -29,7 +28,7 @@ function set_up_the_run {
     (cd $FROM_SRR_SRR;
      rsync -avP rsync://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/${FROM_SRR_SRR:0:6}/${FROM_SRR_SRR}/${FROM_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"    
+    qsub -q budget -v FROM_SRR_SRR,FROM_SRR_GTF,FROM_SRR_REF -S /bin/bash -d $(pwd) -m ae -M donarm@illinois.edu -l "nodes=1:ppn=${CORES},mem=${MAX_MEM}" "$0"    
 };