From 4c50a0cedc2d844127d16d89aae061db9c3af979 Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Wed, 8 Dec 2021 10:39:07 +0100
Subject: [PATCH] test if igv prefs file exists
---
tools/igv_visualize/igv_visualize.rule.snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tools/igv_visualize/igv_visualize.rule.snakefile b/tools/igv_visualize/igv_visualize.rule.snakefile
index 425e190f..ec498c59 100755
--- a/tools/igv_visualize/igv_visualize.rule.snakefile
+++ b/tools/igv_visualize/igv_visualize.rule.snakefile
@@ -11,7 +11,7 @@ rule <step_name>__igv_visualize:
shell:
#plot IGV mapping res
"cd {params.output_dir}; "
- "sed -i 's|DEFAULT_GENOME_KEY=.*|DEFAULT_GENOME_KEY={input.genome}|' /root/igv/prefs.properties; "
+ "if [ -f /root/igv/prefs.properties ]; then sed -i 's|DEFAULT_GENOME_KEY=.*|DEFAULT_GENOME_KEY={input.genome}|' /root/igv/prefs.properties fi; "
"cat <<-EOF > igv.batch\n"
"new\n"
"genome {input.genome}\n"
--
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