From 58d639c831dc88817e35c85bfaace11d3de6c073 Mon Sep 17 00:00:00 2001
From: elabaron <emmanuel.labaronne@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:52:07 +0000
Subject: [PATCH] cutadapt.config : bedtools config
---
src/cutadapt.config | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/src/cutadapt.config b/src/cutadapt.config
index 0c2d60a7..247b34aa 100644
--- a/src/cutadapt.config
+++ b/src/cutadapt.config
@@ -51,3 +51,30 @@ 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'
+ }
+ }
+ }
+}
+
--
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