From a38ea7fe090852d6ff5318937aa8f1087d08575f Mon Sep 17 00:00:00 2001
From: gbenoit <gerard.benoit11@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:48:57 +0000
Subject: [PATCH] RNAseq.config: add bedtools config
---
src/RNAseq.config | 27 ++++++++++++++++++++++++++-
1 file changed, 26 insertions(+), 1 deletion(-)
diff --git a/src/RNAseq.config b/src/RNAseq.config
index 674ad2a..5d56940 100644
--- a/src/RNAseq.config
+++ b/src/RNAseq.config
@@ -50,4 +50,29 @@ profiles {
}
}
}
-}
\ No newline at end of file
+}
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $fasta_from_bed {
+ container = "bedtools:2.25.0"
+ }
+ }
+ }
+ sge {
+ process{
+ $fasta_from_bed {
+ beforeScript = "module purge; module load BEDtools/2.25.0"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
--
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