disabled chmod when building star index

dge_workflow/dge_utils.sh

@@ -494,7 +494,7 @@ dge_create_star_index(){
     jl submit --wait -t 5 -q medium -n "${project}_star_index" "$cmd"
 
     ## prevent further modification
-    chmod -w $(dirname ${star_index})
+#    chmod -w $(dirname ${star_index})
 
     mailme "created star index for $igenome"
 }

dge_workflow/star_align.sh

@@ -12,13 +12,12 @@ Options:
 --pc-only           Use protein coding genes only for mapping and quantification
 '
 
-
 #eval $(echo "$usage" | ~/bin/docopts/docopts -h - -A dopts : "$@")
 #echo "$usage" | ~/bin/docopts/docopts -h -  : "$@"
 #echo "$usage" | ~/bin/docopts/docopts -h - : "hallo dfds"
 #eval $(echo  $usage | ~/bin/docopts/docopts -h - : "$@")
 #eval(exit 64)
-eval "$(echo  "$usage" | ~/bin/docopts/docopts -h - : "$@")"
+eval "$(echo  "$usage" | /projects/bioinfo/holger/bin/docopts/docopts -h - : "$@")"
 
 # v0.7 style
 #eval $(echo  "$usage" | /home/brandl/bin/docopts_v0.7/docopts "hallo")
@@ -144,7 +143,7 @@ dge_bam_correlate . &
 #mysub "${project}__feature_counts" "featureCounts -t exon -g gene_id -a ${gtfFile} -o gene_counts.txt $(ls *bam) -T 5" -q medium | blockScript
 
 ## create tophat mapping report
-spin.R ${NGS_TOOLS}/dge_workflow/star_qc.R .
+rend.R ${NGS_TOOLS}/dge_workflow/star_qc.R .
 
 
 ## Condense counts into matrix