From 876dc0ffd8f5838adaa382ae1f8ea49276282fbf Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 17 Apr 2020 16:19:18 +0200
Subject: [PATCH] solution_RNASeq.config: first test config of singularity psmn
---
src/solution_RNASeq.config | 71 ++++++++++++++++++++++++++++++++++++++
1 file changed, 71 insertions(+)
diff --git a/src/solution_RNASeq.config b/src/solution_RNASeq.config
index a8eb7758..d17bc417 100644
--- a/src/solution_RNASeq.config
+++ b/src/solution_RNASeq.config
@@ -109,6 +109,77 @@ profiles {
}
}
}
+ psmn_singularity{
+ singularity.enabled = true
+ singularity.cacheDir = "$baseDir/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
+ process{
+ withName: adaptor_removal {
+ container = "lbmc/cutadapt:2.1"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = "monointeldeb128"
+ }
+ withName: trimming {
+ container = "lbmc/urqt:d62c1f8"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 32
+ memory = "30GB"
+ time = "24h"
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
+
+ }
+ withName: fasta_from_bed {
+ container = "lbmc/bedtools:2.25.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = "monointeldeb128"
+ }
+ withName: index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 32
+ memory = "30GB"
+ time = "24h"
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
+ }
+ withName: mapping_fastq {
+ container = "lbmc/kallisto:0.44.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 32
+ memory = "30GB"
+ time = "24h"
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
+ }
+ }
+ }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
--
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