use short queue for star

dge_workflow/star_align.sh

@@ -52,6 +52,7 @@ fi
 
 ## build index if not present
 if [ ! -f "${star_index}/SA" ]; then
+chmod -R +w ${star_index}
 
 mailme "${project}: creating STAR index for $igenome"
 mkdir ${star_index}
@@ -87,7 +88,7 @@ for fastqFile in $fastqFiles ; do
     STAR --genomeDir $star_index --readFilesIn $fastqFile --runThreadN 6 --readFilesCommand zcat --outFileNamePrefix ${fastqBaseName}. --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile $gtfFile
     mv ${fastqBaseName}.Aligned.sortedByCoord.out.bam ${fastqBaseName}.bam
     samtools index ${fastqBaseName}.bam
-    " -n 5 -R span[hosts=1] -q medium | joblist .tophatjobs
+    " -n 5 -R span[hosts=1] -q short | joblist .tophatjobs
 done
 
 wait4jobs .tophatjobs