Unverified Commit 656b8f8d authored by Laurent Modolo's avatar Laurent Modolo
Browse files

training_dataset.config: add ccin2p3 section

parent b905d301
......@@ -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'
}
}
}
}
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