training_dataset.config: update psmn config

src/training_dataset.config

@@ -41,53 +41,108 @@ profiles {
   psmn {
     process{
       withname: build_synthetic_bed {
-        beforeScript = "module purge; module load BEDtools/2.25.0"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "BEDtools/2.25.0"
         executor = "sge"
+        clusterOptions = "-m be -cwd -V"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
       withname: fasta_from_bed {
-        beforeScript = "module purge; module load BEDtools/2.25.0"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "BEDtools/2.25.0"
         executor = "sge"
+        clusterOptions = "-m be -cwd -V"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
       withname: index_fasta {
-        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Bowtie2/2.3.4.1"
+        executor = "sge"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
       withname: mapping_fastq_paired {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Bowtie2/2.3.4.1:SAMtools/1.7"
+        executor = "sge"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
       withname: bam_2_fastq_paired {
-        beforeScript = "module purge; module load SAMtools/1.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "SAMtools/1.7"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
       withname: sort_bam_paired {
-        beforeScript = "module purge; module load SAMtools/1.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "SAMtools/1.7"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
       withname: index_bam_paired {
-        beforeScript = "module purge; module load SAMtools/1.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "SAMtools/1.7"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
       withname: mapping_fastq_single {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Bowtie2/2.3.4.1:SAMtools/1.7"
+        executor = "sge"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
       withname: bam_2_fastq_single {
-        beforeScript = "module purge; module load SAMtools/1.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "SAMtools/1.7"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
       withname: sort_bam_single {
-        beforeScript = "module purge; module load SAMtools/1.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "SAMtools/1.7"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
       withname: index_bam_single {
-        beforeScript = "module purge; module load SAMtools/1.7"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "SAMtools/1.7"
+        executor = "sge"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
     }
   }