From 749ddf6478880c036201f6b846e213592c7f0529 Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Wed, 2 Dec 2015 10:42:38 +0100
Subject: [PATCH] removed no longer needed rend.R args quoting

---
 dge_workflow/dge_star_template.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dge_workflow/dge_star_template.sh b/dge_workflow/dge_star_template.sh
index b007fee..d220799 100755
--- a/dge_workflow/dge_star_template.sh
+++ b/dge_workflow/dge_star_template.sh
@@ -121,13 +121,13 @@ rend.R -e $NGS_TOOLS/dge_workflow/featcounts_deseq.R ../mapped/star_counts_matri
 #unpolarised,liver_polar_stage3
 #" | csvformat -T  > contrasts.txt
 #
-#rend.R -e $NGS_TOOLS/dge_workflow/featcounts_deseq.R "\"--contrasts contrasts.txt ../alignments/star_counts_matrix.txt\""  2>&1  | tee featcounts_deseq.log
+#rend.R -e $NGS_TOOLS/dge_workflow/featcounts_deseq.R --contrasts contrasts.txt ../alignments/star_counts_matrix.txt  2>&1  | tee featcounts_deseq.log
 
 
 ## Term enrichment
 mcdir $baseDir/dge_analysis/dge_enrichment_analysis
 $NGS_TOOLS/common/cp_enrichment.R --overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast
-rend.R -e $NGS_TOOLS/common/cp_enrichment.R "\"--overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast\""
+rend.R -e $NGS_TOOLS/common/cp_enrichment.R --overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast
 
 
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-- 
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