From d9d5203ae429fe955dda4daed140663756bf0081 Mon Sep 17 00:00:00 2001
From: hpolvech <helene.polveche@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:47:40 +0000
Subject: [PATCH] RNAseq.confi : bedtools
---
src/RNASeq.config | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/src/RNASeq.config b/src/RNASeq.config
index 0a004ef..87be79c 100644
--- a/src/RNASeq.config
+++ b/src/RNASeq.config
@@ -52,4 +52,31 @@ profiles {
}
}
+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'
+ }
+ }
+ }
+}
+
--
GitLab