From 6bf1544d5c043d44ee3d2a13c556d50eb852effa Mon Sep 17 00:00:00 2001
From: Vincent Vanoosthuyse <vincent.vanoosthuyse@ens-lyon.fr>
Date: Mon, 23 Jul 2018 14:32:56 +0200
Subject: [PATCH] Bowtie 2 config
---
src/RNAseq_sen1D.config | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/src/RNAseq_sen1D.config b/src/RNAseq_sen1D.config
index aa27e45..bd5950c 100644
--- a/src/RNAseq_sen1D.config
+++ b/src/RNAseq_sen1D.config
@@ -65,3 +65,27 @@ profiles {
}
}
}
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $index_fasta {
+ container = "bowtie2:2.3.4.1"
+ }
+ $mapping_fastq {
+ container = "bowtie2:2.3.4.1"
+ }
+ }
+ }
+ sge {
+ process{
+ $index_fasta {
+ beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+ }
+ $mapping_fastq {
+ beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+ }
+ }
+ }
+}
--
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