From 138c254896adbedcc31d74e956f7e05e8c360fc3 Mon Sep 17 00:00:00 2001
From: hpolvech <helene.polveche@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:55:13 +0000
Subject: [PATCH] RNASeq.config: kallisto
---
src/RNASeq.config | 42 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)
diff --git a/src/RNASeq.config b/src/RNASeq.config
index 87be79c..b2b826a 100644
--- a/src/RNASeq.config
+++ b/src/RNASeq.config
@@ -79,4 +79,46 @@ profiles {
}
}
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $index_fasta {
+ container = "kallisto:0.43.1"
+ }
+ $mapping_fastq {
+ container = "kallisto:0.43.1"
+ }
+ }
+ }
+ sge {
+ process{
+ $index_fasta {
+ beforeScript = "module purge; module load Kallisto/0.43.1"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ $mapping_fastq {
+ beforeScript = "module purge; module load Kallisto/0.43.1"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
+
+
--
GitLab