solution_RNASeq.config: first test config of singularity psmn

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/"