use - for stdin

[uiuc_igb_scripts.git] / fpkm_from_srr

diff --git a/fpkm_from_srr b/fpkm_from_srr
index a7ab6e0a4ef9c03c818c9737f1c0a810cc7b87f8..7de768ae2d85a773a8cc198f819e7f871605de20 100755 (executable)
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -9,9 +9,10 @@ function actually_run_the_alignment {
     module load sratoolkit/2.3.5-2;
     module load bwa/0.7.10;
     module load cufflinks/2.2.1;
+    module load samtools/1.0;
     (cd $FROM_SRR_SRR;
-     fastq-dump ${FROM_SRR_SRR}.sra;
-     bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam;
+     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
      cufflinks -p ${MAX_MEM} -G $FROM_SRR_GTF ${FROM_SRR_SRR}.sorted.bam;
      rm -f ${FROM_SRR_SRR}.fastq.gz ${FROM_SRR_SRR}.bam