training_dataset.config: add ccin2p3 section

src/training_dataset.config

@@ -238,4 +238,133 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: fasta_from_bed {
+        container = "lbmc/bedtools:2.25.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+    process{
+      withName: build_synthetic_bed {
+        container = "lbmc/bedtools:2.25.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: fasta_from_bed {
+        container = "lbmc/bedtools:2.25.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: index_fasta {
+        container = "lbmc/bowtie2:2.3.4.1"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: mapping_fastq_paired {
+        container = "lbmc/bowtie2:2.3.4.1"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: bam_2_fastq_paired {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: sort_bam_paired {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: index_bam_paired {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: mapping_fastq_single {
+        container = "lbmc/bowtie2:2.3.4.1"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: bam_2_fastq_single {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: sort_bam_single {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: index_bam_single {
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }