From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 26 May 2015 19:03:04 +0000 (-0700)
Subject: we can only request 18GB
X-Git-Url: https://git.donarmstrong.com/?p=uiuc_igb_scripts.git;a=commitdiff_plain;h=b358c19d627cab411c7b29f415f585adbc456f1b

we can only request 18GB
---

diff --git a/fpkm_from_srr b/fpkm_from_srr
index 34eb304..4b2f90b 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 CORES=8
-MAX_MEM="32GB"
+MAX_MEM="18GB"
 
 set -e;
 
@@ -10,7 +10,7 @@ function actually_run_the_alignment {
     module load bwa/0.7.10;
     module load cufflinks/2.2.1;
     module load samtools/1.0;
-    (cd $FROM_SRR_SRR;
+    (cd "${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 -;
      samtools sort ${FROM_SRR_SRR}.bam -o ${FROM_SRR_SRR}.sorted.bam -T temp
@@ -25,7 +25,7 @@ function set_up_the_run {
     FROM_SRR_GTF="$3"
     export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
     mkdir -p "$FROM_SRR_SRR";
-    (cd $FROM_SRR_SRR;
+    (cd "$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 $(pwd) -m ae -M donarm@illinois.edu -l "nodes=1:ppn=${CORES},mem=${MAX_MEM}" "$0"