From 1c2c4e210832421fa5348012bc634c4fdc67d25d Mon Sep 17 00:00:00 2001
From: gbenoit <gerard.benoit11@ens-lyon.fr>
Date: Wed, 6 Jun 2018 15:06:34 +0000
Subject: [PATCH] add Kallisto
---
src/RNAseq.config | 42 +++++++++++++++++++++++++++++++++++++++++-
1 file changed, 41 insertions(+), 1 deletion(-)
diff --git a/src/RNAseq.config b/src/RNAseq.config
index e35b49a..c646105 100644
--- a/src/RNAseq.config
+++ b/src/RNAseq.config
@@ -77,4 +77,44 @@ profiles {
}
}
}
-}
\ No newline at end of file
+}
+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'
+ }
+ }
+ }
+}
--
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